Not really sure how to categorise this one so I'll explain it as best I can.
I encountered a situation today where I was forced to explore a Lost City Ruin when I did not want to.
The situation was that my trade wagon had been routed across the continent and due to the presence of natives that path had been adjusted by the game, taking me right through a Ruin. It asked me if I was sure I wanted to explore, I clicked no, but as it was the last unit the game just kept repeatedly asking me. The window was modal so I couldn't even select the unit and clear orders, in the end I had no choice but to select yes. Previously I am not sure if the game skipped to the next unit (there wasn't one this time) or just rerouted around (if it's supposed to then no idea why it didn't).
Perhaps a fix for this could be expansion of the options available, so when asked if you want to explore you get the following choices:
Which version of FreeCol? Similar bugs have been fixed in recent versions.
Also, do you have a saved game from just before the problem occurs? It is much easier to make progress on bugs when they are reproducible.
0.11.2 (Revision: 6b10521)
And no I don't have the save sorry. The solution I suggested would remove the problem though
I have built a game with a trade route that is forced to pass through a LCR. With current trunk, the path finding code refuses to route a wagon through the LCR, which is probably the best answer as trade routes are intended to operate without interactive intervention. So AFAICT this bug is fixed in trunk.
If you are able to compile from source, I would be interested to hear if trunk fixes this for you.