I have run into some quirks and bugs while using the editor. I'll list all the ones I can recall...
All these quirks were encountered while using google chrome.
If I save a map, then try to edit data on a city, it doesn't work. The city data window doesn't pop up when I click on the city. If I reload the map, city editing works works fine again....until I save.
The square tool never forgets. If you accidentally click once with the squaretool, then switch to brush or edit, then switch back to squaretool and click ...the first and second clicks form the corners of an unwanted square. I have created some huge monster squares this way, ruining multiple maps. they are hard to get rid of because...
The undo button undoes every terrain eccentricity individually, so if you make a big mistake, you may have to click it a few hundred (thousand?) times before it does what you want.
Editing city income is all kinds of wacky. If you edit a city's income, press OK, leave the city menu, edit the city again, and check the income... you will find that some numbers work fine, others change to random, and some change to other numbers (40 turns into 80 for one).
Things get funky towards the map edges. Creating and then deleting a city or ruin too close to the edge can create an invisible 'ghost city' that can't be erased, new terrain can't be placed on them either.
Water is created in 2x2 squares. This is annoying if you want to create a thin river.