That was most likly a genuine collision ware the 2 mods attempted to change the same value of a Unit, Modswitcher cant desided which change should be used, hopefully a system of resolving these collisions will be added in the future. For the meantime you just need to make shure to dont mix mods that have such collisions.
EDIT - I had another idea that might be of use in a future version, Dependencies!!
As we know lots of Moders are borrowing and extending content created by others, say for example someone adds Saltpeter as a resorce and then someone else makes this Resorce a Pre-requisite for Greniders. If this second Mod gets applied without the first Civ4 will throw an XML error. To avoid this the User should be prevented from merging mods without also merging all of that Mods Dependecies as well.
When you create a merge file you should have an option to enter Dependencies (atleast one possibly more), only other Merge files you already have can be assigned as Dependencies. A new Dependecies element in the merge file holds the information and when you see your checkbox list anything with a Dependency is indented and underneath its parent in heirarchical fashion. Checking a mod with a Dependency will automaticaly check its upward chain of parent Dependences, likewise unchecking the parent will uncheck the child mods. If a Mods Dependency cant be found (cause you removed the Dependency somehow) then a red X is shown in the check box and the Mod cant be selected or merged.