Yes, this problem is really annoying.
I believe that this occurs because when you bulldoze the plot you also lower the ground below the plot removed but not of the road around it, sometimes just a little bit, but sometimes you create very big holes in the ground (I've seen in my game holes with what should be ingame like 10 m depth, next time this happens i will take a screenshoot to post here).
This gap between the road and the ground doesn't let you create a new plot. If you bulldoze a larger area and after that use the terraformer tool to soft the gaps you will be able to create all the plots again in the previous locations ( or at least the most of them ). But sure this is a LOT of work, and your city will surely suffer from this activity......
I really hope that Monte Cristo fix that bug in a soon-to-release patch........, i really hope...
p.s. sry if i misspelled some words, but my english is not that good.