Even if they are doubting the relationship? I mean yes they have a kid together, but I don’t think they have any other proof of relationship other than text messages..
Do you have access to the detailed case notes for the refusal (i.e. GCMS notes)? What do they say?
My guess is that the application wasn't refused due to poor relationship evidence but because IRCC said they weren't common law (which makes sense if they haven't lived together for one year continuously). To be classified as common law, you need to provide evidence that you have lived together for one year continuously. Evidence would normally include things like joint property ownership / join leases, joint bank accounts, joint utility bills. If they have only lived together for a few weeks, they they aren't common law and it makes perfect sense the application was refused.
If they get married, the lack of cohabitation is no longer an issued and the application can be approved without showing a year of living together. They still of course need to provide evidence that they are in a relationship.
Do you have their GCMS notes? What did the GCMS notes say with regards to why the application was refused?