(Putting "scenes" as plural in the topic header in case any more crop up )

WARNING: this thread will contain movie spoilers

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Alternate opening featuring Optimus Prime vs Transit
This does explain why we see Optimus Prime walking through that bus depot in the final cut of the film. It reminds me of The Transformers The Movie where we see Optimus Prime get up off the ground for no apparent reason, because there was a deleted (unanimated) scene where the throws a Decepticon onto the ground right before confronting Megatron.

I do hope that we still get a Transit toy though.