They had some serious cryptography issues (including no perfect forwards secrecy!!!) but they have promised to fix that. I’ve not yet seen any paper analyzing the new protocol. But maybe it could be good?
The seven attacks we have presented highlight fundamental weaknesses in the design of Threema. Indeed, the Threema protocols lack basic properties that are nowadays considered de rigueur for a messenger app to be regarded as secure: forward secrecy with respect to a malicious server, and protection against replay, reflection, and reordering attacks. We believe that the cryptography in Threema has design flaws that need to be addressed in order to meet the security expectations of its users
They have redesigned their protocol since then but again i have yet to see a third party look at it but TBH i haven’t looked into it.