Hi @mlawre
The first run through Stringtie was done correctly, the but second run has the problem.
This priorr Q&A (and what is linked from it) has the details. Stringtie merge error - #4 by jennaj
Please give that a review, and try again. It should solve your problems as well. The parts about running the external annotation through separately, before combining with the others, is important so don’t skip that.
The Help on the tool form explains more but is often missed. 
The tutorial linked from the bottom of the tool form also has a detailed walk-through, with example data and a workflow template that you could also decide to use.