Had this too, started in about 1.05 I believe.
However in 1.05 it happened only with sovereign , now with all units.
First I was thinking I am not clicking careful (exactly) enough on the enemy, but later I noticed that it's enough to wait.
It goes like this:
You have action points for several strikes, the first one is OK, enemy strikes back (or not) but for (before) 2nd and others you have to wait loooong time.
May be the problem is in retaliation (enemy unit strikes back) code, or with the code that "selects" my unit again after enemy retaliated.
Also I had a feeling if you click on your own other unit (try to select it) the wait is shorter, but this might be self delusion 