If this sounds like a wackjob conspiracy theory, it's because this is a wackjob conspiracy theory. Signal's source code and algorithms are open. Just because some government departs have given it funding doesn't mean it's a secret plot by the CIA. 
Signal uses well-known crypto algorithms. If they are insecure, well, then all cryptography is insecure and it doesn't matter which encrypted messaging app you use.
If there's a backdoor in the code, well, the code is open source and people would be able to find it.
Why would the federal government thwart it's own power? Because it's not a unified whole with a single purpose, but a bunch of different departments with different missions that fight amongst themselves. The CIA fights with the NSA and FBI. CIA departments fight with each other.
Parts of the intelligence community wants unbreakable encryption. One reason is nefarious. They want to communication with human intelligence sources (spies), but have nothing more incriminating on their phone than WhatsApp or Signal.
The other is just principles. Several government agencies, the ones giving money to Signal and Tor, want to enable dissidents in other countries (like Hong Kong or Belarus) to able to communicate amongst themselves.
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