Found out what the problem is! Seems I ran into two different problems at once. Had bad luck choosing my airports. 
Problem 1
SimBrief (sometimes?) plans a SID which isn’t a SID.
Example: LIMF/36 N0273F280 SRN6M SRN L615 ADOSA L612 ALBET ALBE2E LIPZ/04R
SRN6M looks like a SID, it is named as one, but it actually is the transition of the SID SIRL6A. This causes (for instance) BATC to end with an error because it (obviously) can’t find the SRN6M SID… simply because it doesn’t exist!
If you check the SIDs of LIMF you will see a LOT of them end with a transition that is named as a SID.
Is this a bug in SimBrief? That is mistakes transitions (which are named as a SID) with an actual SID? I do think SB should plan the actual SID, not the transition.
Another example: LIMF/36 N0275F300 CAN5L CANNE Z651 KELIP KELI3G LSZH/14
CAN5L isn’t a SID but also a transition for the SIRL6A SID.
Problem 2
Changed runway numbers.
Example: LIMF/36 N0275F300 KUK7P KUKEV L50 BANKO DCT VALOR DCT MOLUS DCT SOSAL Z61 FRI FRI2R LSGC/05
LSGC doesn’t have a runway 05 in the sim: it’s 06 in the sim. And hence programs like BATC can’t deal with this. (I think this problem is a flaw in MSFS that may be harder to solve…)
EDIT BATC uses what’s in the sim so in this case Navigraph navdata.