I figured out the cause, my Mac lowers frame rate on low power, which slowed down the animations. It looks like the animations are based on frames and not a fixed time step.
The ash compressor animation has broken for me. At level 36, it says it takes 0.23 seconds but it has suddenly become slower and takes more like 2.5 to 3 seconds.
Is there an issue with the scoring? like integer overflow or something. Getting a new upgrade (plantations trigger once more) caused my score the reduce and lose me the game.