After crashing LRT video rendering time on time I checked the sizes of the intermediate jpegs. It seems that they are slightly different from each other. No more than 2-3 pixels on one side, but enough to crash LRT.

What can I do?

Equilize the crops, this is a problem due to different crop-sizes / aspect ratios.
LRTimelapse 3.3 will now detect this when applying the auto transition and offer you to solve it before launching the renderer.