Can it be detected if a certain unit is in a shuttle? "move locations" can't be used, there is more than 1 shuttle.

Can you explain more?

If you want to detect if any marine is in any shuttle, make a location covering the area/map, uncheck the Ground checkboxes in its properties, and use a 'Bring at least one Marine to location'.

Without locations you can't detect a specific shuttle, nor the units inside, so you'll have to follow the shuttle with a location.
If other shuttles might interfere, give them to another player. At least for as long as it's close.

Ok, how does "move location" exactly work? If the location is big, and moved over a small unit, how does the location position over the unit?

It will be placed so that the location's center is placed at the center of the unit. Ideally, you want to follow each shuttle with a 1x1 location every trigger loop in a way such that it never escapes the location.

Units all have a "center", and locations have a center. Both centers are matched up, unless you're near the edge of the map, where the left side of the location won't go left of the map, and etc...

That means inverted locations will move off the map, but normal locations won't.

Move location centers said location on the leftmost unit of the unit type and player it can find in the given location.
However if 2 fitting units have the same x coordinate, the unit with the highest unit ID (= last created unit) will be chosen.

So if you follow a shuttle with a 1x1 pixel location and they happen to fly straight through one another so their collision box touches the center of the other shuttle both locations will then follow only the last created shuttle.