Timelapse issues on Nikon DSLR?

Well today i shot a timelapse, upon playing it back i noticed contrast issues.

This is the video - I shot on a Nikon D3100 - Any more details needed i can provide.

What's the issue? Is it only how the scene is high contrast?

I can tell straight away from looking at that, that you shot in JPEG format. You're going to have high contrast scenes with inconsistent colour balance when shooting JPEG. You'll want to switch to RAW format to get more out of your shots.

Here's some advice for timelapse videos:

What you are seeing is the exposure change in frames because the lightmeter is seeing different values as the clouds move through the frame. This happens when you shoot in automatic. You can set the camera on manual, pick an exposure but if the light in your scene varies greatly during the time lapse, you risk severe under or over exposure. I prefer to shoot time lapse in manual and let the scene get darker or brighter naturally.