There are 2 problems which persist for some time and I need to point them out. Probably done before but...
Cool-downs for space or ground skills are counting only when u r at space or ground respectively.
For example cool-downs on Call Security Transport(Tuffli) or Call Trade Freighter are counting ONLY when you are in space. I also believe that 1st one only counts while u have Tuffli equipped but I'm still testing that. To make more clearer you need to be in Tuffli in Space for 2h to get it enabled again. This makes Call Sec.Transp. on regular Tuffli usage available on every few days in best case.
Cool-downs on ground skills work the same. U can use for example Shard of Possibilities (generally on end of the mission when things are hardest) and if don't go on ground, 4m cool-down will still await you for it 1st time u enter ground mission.
I don't know if somebody planned this or this is bug but this is really irritating and makes some skill unusable for no obvious reason.
When you finish the mission and your crew is depleted you need to wait IN SPACE(if you are on ground it will not work) for crew to recover. This generally lasts for few min while you can't do anything useful just wait.