I didn't realize we were talking about the Canadian Code....
My guess is the CSA codes have something akin to the old "0.75*rho_balanced" limit from ACI which is also meant to address the overly reinforced concrete members which might be subject to brittle failure. One of the main problems with that limit is that it was based on a singly reinforced section and could not be easily extrapolated into multiple bar layers. Since non-ductile failures can be problematic we wanted to test this even for multiple bar layers, but wanted to let the users know that this section of the code was not fully applicable to their situation.
To test this out I ran your model using the ACI codes (with which I am more familiar).
In the old ACI code (1999 which still had the same type of 0.75*rho balanced limit), I get the exact same warning messages. When I run it in the latest version of ACI, I get messages about the tensile strain at capacity being less than 0.004 per ACI 10.3.5. I'm much more familiar with this other error message. Essentially it is saying that you have an overly reinforced beam which may be subject to brittle failure. Thankfully, this new ACI method (based on maximum bar strain in the outer bars) is applicable in concept to any reinforced section, not just singly reinforced beams. Therefore, the program was right to flag these members in this way.
What you do now is less clear to me. It may mean that you need to reinforce it more like a column with more closely spaced ties and such. It may mean that you want to increase member depth. Maybe you decrease the reinforcing.