Some of my favourite red flags:
Signal's dependence on Google libraries: https://github.com/signalapp/Signal-Android/issues/9044#issuecomment-535194837
Signal dev bullshitting a non-answer and then hilariously refuting his non-answer: https://github.com/signalapp/Signal-Android/issues/9044#issuecomment-534340623
Signal hiding its serverside source code for many months: https://github.com/signalapp/Signal-Android/issues/11101
You can find many more examples.
The last one about server side code, together with Signal's funding sources and their obsession with phone numbers code leads me to suspect that Signal is just a honeypot by US intelligence.