If you want to repair the Mako but don't want to waste Omni-Gel doing so (or you simply don't have the time to waste waiting for the repairs to process), you can always press X and opt to return to the Normandy. It will inconvenience you since you'll be reinserted in a specific place when you decide to go back to the planet in question, but your Mako will be fully repaired for reinsertion.