I'm on 1.15 and have noticed this alot ... don't recall a lot with 1.12 or 1.05, but with 1.15, it's really getting annoying. I'm constantly having to select-all, leave-fleet, create fleet b/c I find my disciples joining up with my carriers, or illum's joining up with my guardians...really annoying. The only fleet which didn't appear to to get mixed up was the purge vessells.

The other thing I've found is that while two fleets are seperate, when I give a move order to one, another fleet does the same move order. WTF??

Yeah, big problem.  A issue I have had with tec (im running 1.15 and ent 1.01), sometimes my fleets flag ship dosnt jump with the rest of the fleet (yes they are all set for a linked jump) for some reason (probaly redocking fighters or turned the wrong way) and it takes a few secs longer for it to jump.  what happens is that the rest, or part of the rest of the fleet will try to jump back to the grav well that it was before (tring to "reform fleet") and when this happens in a grav well with a jump distortion node, they get chewed up badly (really badly with enemy star base near by).

What needs to happen to fix this issue is to fix the formation errors (like making all the ships face the same way when not in combat).  What would be nice is to have a formation tool that lets you choose from a set of pre-determend formations, not just tight, standard and loose (like line, cercle or triangle formations) and be able to move then face your fleet, instead of each ship just facing away from its prevoius location.

No bonuses that i know of.  to fix the flag problem, select all your ships that you want in your fleet then push the tab key until the ship you want as your flag is selected, then use the create fleet option.  It should now be your flag.