Have also posted this at the Sourceforge bug tracker.
Running latest Triplea - 1255
Neither of these bugs are a huge deal, and can be handled with a simple edit.
#1 American Fighters on British Carrier.
If American fighters exist on a British carrier, *and* there is a British carrier built but not yet placed, *and* if you move two British fighters into the SZ with the Brit+American carrier fighter combo, the Brit fighters WILL disappear before the 'place new units phase' despite the warning window popping saying they have one carrier on which to land. This bug is easily reproducible by toggling through to the Brit turn, a few edits, and one carrier build in the cue.
#2 Sub movement bug
I often take allies with a 6 bid and put a UK sub in SZ 35 (off of India). I often wish to move to SZ 49 (off of Borneo) to sink a transport there. However, Japan often puts his destroyer in SZ 38 (East Indies) and places some fleet elements in SZ 37 (off of Burma). If I try to move to SZ 49 in the above scenario, it insists I go through SZ 38 (where the destroyer is) and hence am blocked, and if I try to to take two "one steps" through SZ 37->SZ49 the engine wont allow me to take my second step.
#1 can be solved with edit in the mean time, tho it should be fixed at some point
#2 is not really a bug. simply hold down CTRL while clicking the route you want to take. let me know if you can figure out how to do it or not, its rather easy and is in the game manual "movement help" which noone reads (its called using a way-point)