As I understand that Croatia is not in Schengen Zone, where do I get a passport stamp if I arrive/depart Croatia via ferry or bus to small town?
I entered Croatia on a bus from Portoroz, Slovenia. The bus stopped briefly at a border station (like a toll booth). I didn't have to get off the bus, the immigration person came on the bus and I just showed my passport. I don't recall if my passport was even stamped there. I just looked at it, and I see Croatian passport stamps for our day trip to Montenegro (stamped both leaving and then coming back) and also for our departure when we flew out of Dubrovnik. It's possible that they didn't bother with a passport stamp when we were entering Croatia on the bus - if they did stamp it, it must have faded very badly because I do not see it now.
Short answer is: they'll check your passport at the first immigration station you reach, at a booth on the highway, or in a ferry port.
When crossing between Croatia and Schengen Area countries (Slovenia, Hungary) there should be a manned border post and non-Schengen/EU passports should get stamped in and out. On a local bus or ferry, nearly everybody will be EU citizens (locals or other Europeans), and they have no restriction, don't have their passports stamped and can even cross the border using their national identity cards.
A border guard may get fed up of checking passports/ID when everybody is "access all countries", and if it is the local bus just look in through the window to see if anybody looks like a refugee (which is who his bosses are really interested in stopping). That way the one non-EU tourist on board doesn't get their stamp. I have seen this happen.
On road borders it may be a shared border post, two different uniforms but only one stop.
My concern is that I will be maxing out my 90 days in Schengen and want to be sure that I get properly stamped in and out while from Croatia. I will fly into Dubrovnik but likely bus out of the country. What will happen if I don't get stamped out of Croatia regarding the Schengen limit?
Sally, not getting stamped out of Croatia should not be a problem. Not getting stamped into the Schengen Area (into Slovenia) will not be a problem at the time. It may cause problems when you later leave the Schengen Area, as you will have no stamp to show how long you have been in the Area.
I suggest you keep your bus ticket, or whatever other proof you have, Just in case you don't get stamped, AND you get questioned on exit.
...and, when entering/leaving the country, they will at least look at your passport. Make sure it gets stamped then too. I can't imagine they would not do that if you ask.
Thanks for feedback!
If you are running tight on your Schengen days remember that arrival and departure days count as part of the 90, even if only a few minutes before or after midnight respectively.
They don’t generally stamp at the land borders in Croatia anymore. It’s all computerized, so the data is there. Last few times for us, they just looked at our passports and handed them back to us after scanning them.