I have no idea how to reproduce this. It's only happened to me once, but it was pretty bad! Here's what happened:
I was playing level 14 (Standing Orders) and was quite a ways into it, with many towers built. Then the aliens began to overwhelm me and take my cores, so I pressed Backspace to go back to my previous checkpoint. The screen blacked out and faded back in and every single one of my towers came out of the ground as if it has just been built or upgraded. Upgraded towers were still upgraded, but they all had to come up out of the ground.
This gave all the aliens about 10 seconds of free time to run past all my towers without any consequence.
I tried reloading again and again but it did the same thing every time. Eventually I had to just restart the level.