I had the same problem with the Phonecian port but in a lake. 

Other small graphical glitches:

• The highlight box around a unit in an army was frequently mis-sized, sort of doubling in height and extending below the unit portrait if you click on it multiple times. Couldn't reproduce this one after the early game though. (Reproducability: 1/5) 
• Playing in a non-native resolution caused cursor size flicker (Reproducability: 4/5)
• Playing with a controller plugged in also caused cursor size flicker (Reproducability: 2/5) 
• Icons for available constructions disappeared at several points throughout game, (but could still hover them to get help text and could still select) couldn't figure out what it was related to. (Reproducability: 3/5) 
• I had one city where the central plaza disappeared early game and then never showed back up (Reproducability: 5/5: save files: Khmer Turn 98.ctr, Spanish Turn 125.ctr) 
• Many cities' walls disappeared from the map visually  (Reproducability: 5/5, see Spanish save above) 
• Unit movement bugged out in mid/late game, they would not move visually but their movement would be exhausted and if you issued another move order it would come from the place the game clearly remembers them actually being (Reproducability: 2/5, sorry I don't have a save for this one)

Edit: a couple more:

• Load screen always says "Neolithic"/"Nomadic" for your empire no matter when it happens (Reproducability: 5/5, never went away, see any above save)
• Save times on the load game screen are apparently reported in UTC rather than local system time. I commend you on saving as UTC on the back end, now you just gotta close the loop ;)