I had a similar thing happening at a crossing from Croatia to Slovenia. Two sequential sets of booths. Went through first set fine. They checked my passport, etc. Second set was unmanned. Went through. Immediate sirens, flashing lights, etc. Went back. Got yelled at for not stopping at customs. First booth was immigration, second was customs. Not that they have any signs on them or anyone tells you that.....and considering that in the EU you just roll through borders. Even at US/Canada crossings there's only one set of booths. Funny place.
Glad to hear you enjoyed Dubrovnik. Did you get to that bar that hangs outside the city wall over the sea? Pretty cool place and a good escape from crowds although it can get crowded there too. Hit it when you go back. I went there a few Octobers ago....fewer tourists (like me
). If you decide not to stay in hostels you might want to consider staying in the little village that is just north of the main gate into the old city. It's nestled between the road to the new town and the sea, scrunched into a tiny little cove. It's pretty quiet and gorgeous, as you have the city walls looming to your left (as you face the sea) and a castle on top of the ridge to your right. For accommodations there is a restaurant on the right, up a little bit from the shore, that also has rooms. Ate breakfast there in the morning and talked to some folks from England who were quite pleased with it. The other alternative is to find George and get a room through him. George lives in the village but seems to be the major fixer in the city. He meets every bus when they stop by the main gate to discharge tourists and hits people up with offers of rooms. I stayed in one of his, which was in a private house. Room was very basic but the view was stunning: window opened directly above the tiny beach. George is actually a very nice guy and is a single-handed tourist agency. His enormous wallet is crammed with brochures, ferry schedules, and business cards. He hooked us up with an excellent restaurant in the old town when we asked him to recommend a place where locals would eat, and he saved us much aggro re getting a ferry out to one of the islands. I still remember sitting on the terrace of the restaurant in the cove and hearing my name called from far away. Looked up and saw George high up on his balcony a block away giving me a big wave.