With .23c:
The scout bonus against animals (+50% appears to be being counted twice. My unupgraded scout (str 2) attacking a wolf pack (strength 3) in an emperor level game displayed combat odds of: 3.00 vs 2.00. So the scout received a 50% boost and the wolf took a 33% hit (2/3) in strength.
But wait, there's more:
-Warriors are getting their +25% city defense when attacking out of a city.
-Both the attacking and defending unit get +40% when attacking across a river.
-Bonus vs. barbarians on lower difficulties is applied twice just like the scout bonus.
-I'm sure there are others as well, but those are the only ones I've really looked at.
After a bit of testing this is what i have found:
Mouseover combat window:
-the inappropriate boni are not listed
-they are represented in the effective strengths of the units
-the combat odds are sometimes calculated correctly (despite the incorrect effective strengths)
-the combat odds are sometimes calculated incorrectly (but are consistent with the incorrectly listed effective strengths)
Combat log:
-the inappropriate boni are not listed
-they are not represented in the effective strengths of the units either
-the combat odds are sometimes calculated correctly (and are consistent with the correctly listed effective strengths)(this matches what was listed in the mouseover combat window)
-the combat odds are sometimes calculated incorrectly (despite the correct effective strengths)(this matches what was listed in the mouseover combat window)
-regardless of the odds listed (correct or incorrect) combat occurs with the correct damage dealt and correct chance to hit
That last point means that despite all the miscalculation this appears to be a cosmetic issue (albeit one that will cause incredible confusion), since the actual mechanic of combat appears to be unaffected.
mindlar (or anyone else that wants to help confirm this), if that happens again check the combat log window. The scout and the wolf pack should each be hitting each other for 20hp, which is the case when relative strengths are 1:1. (they should also hit each other an equal number of times (roughly) but you wont be able to see this in the course of a single battle).
Another easy situation to check is an unpromoted warrior in a city attacking an orc spearman, the warrior should appear to get an incorrect +25%, but the combat odds should still show 20hp damage being done per hit, thus meaning 1:1 effective strengths.
One last note about the combat log: the listed odds are from the perspective of the attacker, while the list of boni are from the perspective of the defender.