Something I've noticed is that if you change the name of a connected portal and then go through it immediately you will get sent to the portal it was previously connected to instead of teh location you just entered. Ended up in couple situations like the OP before I got into the habit of giving the portal a good 15-20 seconds to fully update it's connection.

Another thing I did was make an unconnected portal named FUBAR as a back up for situations like that. If I get sent some where unexpectedly I can just rename the local portal to connect to my emergency portal and get back to base. Then immediately clean up the name of the remote portal once I figure out what happened so FUBAR will always be ready to save my bacon.