Confrontations like these make running captains lose heart. (3-3)
I believe the answer is:
run-ins
'confrontations' is the definition.
(I've seen this in another clue)
'these make running captains lose heart' is the wordplay.
I cannot quite understand how this works, but
'running' could be 'run' (synonyms) and 'run' is found in the answer.
The remaining letters 'ins' is a valid word which might be clued in a way I don't see.
This explanation may well be incorrect...
'like' is the link.
Can you help me to learn more?
(Another definition for run-ins that I've seen is " Disagreements or fights, with officials perhaps".)