Station garrison is just one of the many repeating planet projects that IMHO shouldn't repeat, or that we should at least have an option not to repeat. My latest gripe is playing as a synthetic race I tried to build just one more population on one planet and a couple of turns later discovered that all my durantium had disappeared.
That's exactly what I would suggest. I know the project mechanic was changed some time ago because of some vocal people that resented to give fully developed planets new orders every couple of times when a project came to a close, but while that is only a bit annoying (not for me, I must say), the current system with auto repeating projects is downright harmful if you forget to check on your planets every turn: in case of "normal" projects like Aid Research you lose production if you have to cancel the project because you can now build something else for what you waited by initiating the project, but in case of Station Garrison if you station too many legions you cannot retrieve them anymore and they are lost for war.
I agree the best solution is to introduce an option to specify for every project whether it should be repeated or not. But Stardock seems more than reluctant to make UI changes (like more sorting options in the various lists, an indicator how far a ship can move, changing the default auto improvement setting to "only when all tiles are full", giving a choice at colonizing a planet where to put the colony capital and so on ...). It's not clear to me what makes that so difficult but it really must be very, very difficult
As to disappearing duratium: I hope that (and all other occurences of resources being deducted every turn instead of once) will be fixed soon, because such a problem would ruin the game for me.