This happens to me alot as well, heck I can have my transports parked 3 sectors away next to my own planet, in my own influence space and they do that.

The AI isnt smart enough to use its own influence area as a basis for those function checking I suppose. (which it should)

When playing with the easier difficulties, I've gotten warnings when having transports parked next to my homeworld because I was upgrading them to a newer version.

Their AI for transports really does need an improvement. I have both extremes--sometimes I do get the problems already mentioned, but the transports I usually use have a movement of 65. I can take over enemy worlds from two sectors away, and even though they can see that I have transports within one jump of their worlds, they're not bothered because they have nothing (but a scout ship and a freighter) "near" the transport. I could see this happening when I use a "warp gate" (16 military starbases in a sector corner, all them with +2 ship movement, brings my Hammer of Dratha transports up to 97 movement for one turn, mwahahaha...), but they SHOULD be checking "does player civ have known transports within two jumps of our planets?" rather than "are any transports within sensor range of any of our non-ships?"

Edit for spelling.