I have run into the first one about the formations before. It is caused when your formation file doesn't have a formation that the AI file is calling for. To fix it just go in there and make a formation called Compact. Alternatly go into the AI file and alter the formation is used by default.
Without more of the error message on the other one I can't help much. But it sounds like the same basic thing cept with AI ship design creation. Alot of them say they are compatible with 1.41 but in fact require a few small adjustments.
If you get the TDM modpack which keeps all the original techs etc but alters AIs and a few other minor things like the formation file then it very well might solve all your problems.