Heres a few synonyms:
If its the trouble where you’re having difficulty or problems: (im having trouble doing this work) you could say something like difficulty or problems
if its where its somebody causing a disorder: (he is causing trouble) you could say disturbance
if it’s where its troubling someone: (this had been troubling her for some time) you could say bothering, bugging, concerning, disturbing, annoying, irritating, etc.
*with our without suffixes depending on the way the sentences are worded but its really obvious* :) <3