I suppose the easiest way to "fix" this, if anything is needed at all, would be to replace the craft with spawn tiles - if that works for that specific kind of mission. Then you can just explain this so that some vehicle dropped them nearby to avoid detection and they just walked on the mission site. The only a little bit shady aspect with that might be how they carried the huge loot pile on the site...
If needed, a similar approach can be used with some other missions as well, if there is any need to make any mission harder (= no turn 1 or later cover provided by the craft).