We still don't know everything we would like to know about the human body or have the technology to find this out, one doctor can deem an abnormal test result enough to fail a medical whilst other doctors might not see it as a problem. There are differences in what is acceptable and what is not between hospitals within 10km from where I live (everywhere else too), I assume that for topsporters these margins are smaller but still there.
Also depends on what he failed the medical on, it could be an old injury which didn't heal correctly or a potential problem for the future which the club didn't want to risk. Some clubs don't want players with slight heart problems, others take that risk and try to minimise the damage it could do.