You will need to re-save the return for that period in QuickFile otherwise it won’t let you submit the next one. If you disable online filing in your account settings then you should be able to create and save a new return for the relevant period, then turn the setting back on again.
However you need to make sure that what you save matches what HMRC think you have submitted. You may need to make manual adjustments to some of the boxes, then you’ll have to apply the same adjustments in reverse next time (e.g. if you have to subtract £20 from box 4 to get it to line up then you’ll have to add £20 to box 4 on your next return).
If you disable online filing first in your settings then you should be able to “save” the return in QuickFile without “submitting” it to HMRC. You have to do this in order to lock down the relevant invoices/payments otherwise QuickFile will try to include two quarters worth of items next time you submit.
This is not a bug - QuickFile always includes in your next return any items dated within a previous period but that were entered into QuickFile “late” after you’d already submitted that quarter’s return, to make sure late entries are accounted for at the earliest opportunity.