Rubber roofs are supposed to be glued down, but often there are areas that are not attached to the decking; these small areas or "bubbles" don't seem to cause problems. Are your soft spots due to deteriorated decking, or are you feeling the elasticity of rubber roof material that is not glued down? Do you have any evidence of leaking? Does the seam between the front cap and the roof look to be in good shape? Do you have a dealer that you trust who could look at your roof and help you decide if you have a problem that needs fixing?
Here's a couple of pictures I took of my new trailer, and asked my dealer to look at. According to them, there is no problem.
There's lots of advice and information in forums... sometimes it is correct. For example, all of my posts are made by a political appointee who got the job as a reward for contributions to my diesel bill.
2011 Jayco 28.5RLS; 2008 Chevy Duramax; Pullrite Superglide Hitch