It is a well-known bug that is quite easy to work around. The key is getting the fragment that you have already transported to become the main part of the unit. This is achieved by interrupting the air transport of the unit for one turn, after more than 50% of the load value of the unit has been transported to the new location. Once the transported fragment has turned into the main part of the unit, you can resume air transport without fear of the bug striking.
If only it were so simple!!
I have units that keep switching back and forth between fragment and parent, for no discernable reason. In the most recent example, i was trying to evac Asiastic fleet from Borneo and there were 300+ support squads in Darwin, and some in Borneo. One turn, the Borneo fragment would be a fragment, and then the next 5 or six turns it would turn into the parent, then turn into the fragment again, then the parent, and then the fragment. I lost a couple of units this way because i thought i was safe to transport them after they turned into fragments and then they disappeared (apparently after they turned back into parent when i wasn't paying strict attention).
This disappearance caused me to implement rather drastic measures in trying to evac or move LCUs, and consequently i've discovered all kinds of irregularities occuring in the process. This also causes it to be a huge time sink!!
One other irregularity i've found that occurs with regularity is that the last few squads to get transported will end up being mortars or mg squads, with negligible load costs, but they will NOT get transported unless there are more units around. I.e. - transport a unit by air from say Manilla to Jesselton (replacements off) - get the ENTIRE unit to Jesselton, but then the MGs (or mortar) squad sit around no matter how many AC are assigned to transfer them. Very frustrating to keep trying to move these guys without results.