Twixtor glitch after rendering

What Rick said - Twixtor uses GPU acceleration, AE does and so does AME. You're stacking stuff on top of each other and may simply exhaust resources. It may be necessary to switch stuff to software-only rendering, be that Twixtor's effects settings or AME's encoding.

Mylenium

Applying Twixtor directly to a footage layer is not the best or recommended workflow. Add a new solid, Apply Twixtor to the solid, point Twixtor to the layer you want to retime. The results are a lot more predictable. 

You may also want to check your GPU. It may not be supported through the Media Encoder's background rendering system.

I've cleared all memory and cache in after effects by the way.