If you are not able to edit a deal's Stage field value, it could be because the Probability field has been removed from the Deals module.
A deal's Stage is defined by its Probability. For example, you have defined the stage 'Negotiation" by a Probability of 10%'. If you remove the Probability field altogether from Deals, then the deal Stage has no definition and therefore is no longer editable. In order to be able to edit the Stage, make sure that the Probability field is included back in the Deal Information section.