I have that feeling, too. I once rebased 3 Navs from Kiel to Brest and in the channel they got intercepted and 2 were destroyed and one was down to 20 strenght.
I think the problem is, that you can't retreat air units from any kind of battle with the new patch. You just get the message "UNKNOWN STRING WANTED", which is really annoying as you can neither retreat Bombers while when they get mauled nor give them new orders while in attack.
I was also not able to produce escort fighters. When that event popped up I didn't choose the escort option since I thought, I'd get another chance later but nothing happend unitl 1942 so far.
Besides from that I must say that the game is a little bit boring to play as Germany from 1941 on. I totally smashed SOV within a few months. After a two months or so my mobile forces had created several pockets and advanced hundreds of miles with totally unsecured flanks, which wasn't a problem at all, as the Russian troops were just to slow. Fighting for fortified cities like Moscow took only a few days (it was surrounded though). However, by December 1941 I had destroyed probably 60 Russian divisions and had taken Baku and Stalingrad (both fronts were almost totally undefended after my panzers had torn a huge hole into the frontline), Moscow after a bit of fighting and Leningrad was surrounded and cut off.
Bitter peace came in April 1942 or so, after I had finally taken Sverdlovsk.
At that time I was already in peace with Great Britain, which surrendered in early 1941 after my forces had overrun Palestine and Seeloewe was succesful (and quite easy). Japan had almost defeated Nat. China then but wasn't at war withe the USA. I have now 700 IC and have absolutely no idea how to spend them! I already have a huge navy, army and airforce. I just don't need to build anything anymore.
I'd have a request aswell: It might not be possible to realise, but it would be better, if one could distinguish the brigades that share the same model. Like engineers and pioneers, or motorcycles and armoured cars etc. I find it quite annoying to not be able to know, what I'm looking at. I can't rename f.e. "12. Infanterie-Division" to "12. Infanterie-Division (AC)", because the game doesn't recognize it and will build another 12th Inf. Division...