Do you notice the subtle flickering in this time lapse? I figured out the issue thanks to a web search. Turns out that using a lens with an electronically controlled aperture, as are most modern DSLR lenses will cause this, even when you set the aperture in manual mode. It’s the result supposedly of the camera sending a signal to the lens aperature at every frame. When the signal is interpreted by the mechanical aperture, very slight fluctuations in the amount of light entering the camera occur. To fix this you can do one of two things.
1. Use a fully manual lens. I am using fully manual Nikon lenses on my Canon now for time lapse. Adapters are available.
2. Use software to fix the problem in post. Granite Bay Deflicker is a popular choice. Seems to work OK.