Most common reason for this is power-management.
If, for example, you've got an exploration ship where there's only enough power to activate the SRV hangar if the thrusters are shut-down.
You land, the thrusters shut down, you activate the SRV hangar and deploy the SRV.
Your ship will magically take-off regardless of power-management.
When you recall your ship, power-management
does kick in, your ship will still have the SRV hangar activated and now it'll decide that means there isn't enough juice for the thrusters and it'll fall out of the sky.
For exploration ships, in particular, it's just not worth the risk of min/maxing power-management.
I usually go for overcharged PPs rather than anything else, simply because it means you can just mod' it up from, say, G2 to G3 with minimal consequences (if you're using the Thermal Spread XFX) if things are too marginal.
Incidentally, it used to be that you could deliberately take your thrusters off-line and your ship would remain parked on the surface regardless of how far you travelled in the SRV - which was quite handy.
Dunno if that works
properly again now but I stopped doing it 'cos sometimes your ship would take-off magically and then, once again, when you recall the ship the thrusters
will be offline and it'll crater.
+EDIT+
Here's a pic' of my Phantom re-enacting the famous "running away" scene from Prometheus.
In the module-management HUD, it always used to show the power-usage bar in red (indicating there was a problem) but in use it always seemed like I could set the power priorities to avoid any problems.
Then this happened 2 or 3 times.
Increase Overcharged PP mod' from G2 to G3.
Problem solved.