It would depend on the country. If you got a passport stamp, you've "been in" that country. Transiting say...Panama, you never clear any kind of customs. But transit Mexico, and you do enter the country and get stamped. So it would likely depend on the country. If you didn't have a stamp (easy visual cue) or didn't cross customs (where your passport would be scanned and registered, even if not stamped) then they'd have no idea really. Airline officials would know where you connected, but it's customs officials who would allow/deny your entry to a country.