I did some tests related to workers and tile improvements and came up with the following list of possible bugs (I used SVN revision 5218). Please note that since there is no specification of the system I have no idea what is a feature and what is a bug, therefore I'm listing everything that seem inconsistent or counter-intuitive.
Thanks for this. Yes there are problems with improvements and terrain features. I started adding then both without understanding either.
There are inconsistencies in how building certain improvements does or doesn't remove terrain features (Forests, Jungles, etc.) on that tile. Often, early versions of certain improvements do not remove forests therefore it's preferable to build an early version of the improvement and upgrade it through being worked by nearby city. This requires disabling of hiding obsolete worker improvements in BUG menu and even with the option disabled later workers are usually unable to build the old improvements. I've tested which improvements remove which features and the results are in the attached file (sheet Feature compatibility).
There are inconsistencies in whether or not certain improvements are buildable on certain combinations of terrain types, features, etc. I've thoroughly tested this as well and the results for Workshop, Cottage and Farm are also in the attached file (on their respective sheets). Other improvements seemed fine, or the inconsistencies were minor and are mentioned later in this post.
There have been many discussions back and forth on if improvements should remove jungle/forest or not. One thing I have not done is add code to remove the jungle/forest when the improvement upgrades from one that does not remove it to one that does. I should be able to do that without worrying about what the improvement is just what is being removed and when so I can give the correct number of hammers.
Some terrain features need to be removed before something can be built rather than having the removal on the improvement. An oversight on my part.
The new workers - Llama/Mammoth/Camel Workers cannot build Tree Nurseries unlike the other workers of that era (regular Worker or Mule/Elephant/Buffalo Workers). Industrial Era Workers are again able to build Tree Nurseries.
Tree Nurseries are an optional mod and the person adding the new workers probably forgot (or did not know) that they had to update the mod also.
The "improved" Forts (the ones providing +75% and +100% defense bonus) are only buildable on the terrain types form the original game, while Forts are buildable on every terrain type.
Should be.
Not sure if the Tree Nursery improvement, after growing into Young Forest and later into Plant Forest, should also place a forest feature on the tile as does the late game Plant Forest worker action (available when terraforming/reforestation option is enabled), but it doesn't.
I thought I did both. Obviously not.
Tree Nurseries cannot be built on Marsh, even though it's possible to plant all types of features on this terrain type (Forest, Savanna, Bamboo in late game with the terraforming/reforestation option enabled). On Permafrost, it's possible to build Tree Nurseries, but it's impossible to plant any features.
Again because it is an optional mod it got forgotten.
With the Usable Mountains option enabled, when mousing over a Mountains tile, the tooltip doesn't display its terrain type or features on it (most likely because in unmodded Civ4 mountains are never usable). It's often impossible to tell what improvements will be be buildable on Mountain tiles, because some are only available on certain terrain types. It would be great if this info was displayed in the tooltips or at least if Mountains ignored terrain types altogether (they have the same yields for all terrain types anyway).
The New Forest terrain feature (not sure if it's currently supported by any map generators) cannot be removed except by building certain few improvements on that tile. It also doesn't allow building of any Lumbermill-type improvements.
It is not supposed to have improvements on it, you have to nurture its growth by working it, then you can do what you want with it. It is not supposed to occur at map generation.
We also have a burnt forest that, with new forest, is supposed to be used with the forest fire and volcano events.
Cacti terrain features (again, not sure if it's currently supported by any map generators) cannot be removed at all, only by planting another feature over it.
Windtrap improvement seems like a late game version of the Windmill improvement, but cannot be build on Mountains even though Windmill can.
It's possible to build Lumberjack and "Gather Wood" (the first tier of the improvement) on Jungles, but it's impossible to build Lumbermills.
Jungle tile feature seem to block building of many different types of improvements on certain terrain types (see the attached file for more details), it also appears that you cannot build the Ancient Relics special improvement on Jungle tile. This is quite strange since it can be removed by chopping it down and the improvements can be build there afterwards. Similarly for Swamps and Peat Bogs.
There is a problem with limiting improvement by technology which may be causing this problem. If something is on marsh and has an improvement that can be built there but you don't want the improvement built on swamp because you can't remove the swamp until a later tech then you need two improvements and we may not have done the second. Eg you can build a cottage on marsh if it has fresh water when you get the tech for cottages if we put the remove swamp on that improvement then you would be able to remove swamp long before you should be able to remove swamp. This is probably the reason for the other similar cases.
Rapa-Nui Workers' pedia description states that they should be able to build special Moai improvement, but they cannot. No such improvement seem to exist either. They can also build Highway and Jumplane, but cannot build Railroad, Electric Railroad and Maglev (these seem inferior to Jumplane).
That means that they forgot to tell me that they wanted the Moai improvement and provide me with a link to the graphics. (This may be a solution to the "geoglyphs" problem I am having ie have a worker that requires the Nasca Lines wonder.)
Different worker units are supposed to have different work rates (and they appear to), but these work rates don't seem to be displayed anywhere. This means it's impossible to tell how much of a work speed upgrade are you getting when upgrading workers without extensive testing.
It is just a number, the larger the number the faster they do stuff. Since with promotions it will vary by unit they probably need it in the hover over text. I can add it to the pedia, I think, which will be the work rate unadjusted for wonders or promotions.
For some reason the Buffalo and Elephant Workers cannot Burn/Remove Bamboo unlike Work Mule and Dog Worker (same tier workers). They all share other worker actions.
An oversight.
Entranced Workers (the cheap worker units trainable with Voodoo as state religion) are not tagged as Worker type unit and while they are able to earn experience, they are unable to purchase any promotions, since they have none available.
Another oversight because Voodoo is optional and so are their workers so the XML is in a mod.
When attaching a Noble (and possibly Great General) to a unit, the experience points from the Noble are also shared with worker units on the same tile.
Probably not what was intended.
Its not really that bad, not as bad as not improving the land, but i'm just curious why she is doing that. 
I think it is in my current game) its definitely worth it. Having extra improvements earlier than your opponents is a sizeable and very tangible advantage. Lets say you are working a hill and an opponent is working a hill with a prehistoric workshop thingy, they'd be getting like +3 or 4 hammers per turn. Over 50 turns lets say thats 150
before modifiers! If they are building military units as an example, they could easily have +40% modifier thats 210
