There is a website dealing with people who masturbates in prone position. Some are in favour and some are in disfavour.You may search for this website.
While this method is probably common, I would stop doing this sort of masturbation if you have a hunch that it is causing your problem. Since you are "sexually active", I also recommend that you stop all masturbation, and you will probably have more satisfying times when you do get sexually involved with your partner.
Ive been doing this regularly since I was 13, and now i'm 22. I'm now sexually active but I still do it. But i realise my erection is weak on the bottom part of my penis.
Probably not but how long ago did you do this and what is your age? Any other symptoms? Get your testoterone level checked. Another possibility could be you have Vericocele Veins in your testicles. A Urologist can check for these.