What should I do if wrong version of manuscript was uploaded and submitted to journal?
The odds are very good they'll let you do it. They have nothing to gain by sending a badly-formatted manuscript for review. You could even submit the correct version as a separate submission now and the most that'll happen is some minor inconvenience for the journal staff (this is when the duplicate submission flag kicks in).

Worst case scenario, you can withdraw your submission and resubmit with the correct version.