Most likely your boyfriend was born with hypospadias, a relatively common abnormality that may affect up to 3 in 1000 newborn boys. Instead of having a urethral opening at the end of the penis, boys born with hypospadias have an opening on the underside of the shaft.
If this is a problem, the condition can be surgically corrected. Often, surgery is arranged before the child reaches school age. The surgery, performed under anesthesia, involves using a small piece of foreskin to fashion a tube to extend the urethra to the end of the penis. The original hole is most often left as is since the urethra now bypasses it. This probably explains why your boyfriend's penis has two holes; only one is functional.
Have you tried asking your boyfriend about the two openings? He has surely noticed that his penis has two holes and probably knows that this is rather unique; and, if he had surgery, perhaps his parents never told him about it.
It can sometimes be embarrassing to talk about genitals, even with our partners, but open and honest communication is an important part of any healthy relationship. Who knows, maybe once you bring up the subject, he might have some questions for you!Alice!