There are lots of articles about dip stick and Lab culture tests not picking up infections. I frequently get culture reports that say no action or borderline, then a few days later get positive results and I am given antibiotics.
I have a permanent Catheter so am more prone to infections. A pain in the gland or bell end is a frequent experience I have when an infection is present. Following a pain in the gland i often pass visible debris in my urine and at times a yellow discharge, but still get negative cultures. I get a particular odour when I have an infection, the smell is a bit like stale smoke.
Another cause of the pain in the gland of the penis I have experienced after surgery was a kidney stone, more painful when actually passing urine and such a relief when it pops out.
So soon after surgery things are probably still healing and debris stuck in the urethera may cause pain.
Less likely but experienced by a few of us on here is migration of surgical hem o lok clips. Supposedly quite rare but it is perhaps more common that we are led to believe. There has been guys who pass the clips naturally. I had three removed surgically.