A wife's place of legal settlement depended on her husband's. So normally you would expect them to be in institutions that belonged to the same poor-law union, though not necessarily in the same workhouse within that union.
A few reasons why a married couple might be in institutions in different poor-law unions ...
* they had not been living together for a while and did not admit to being married
* the husband could not be located (e.g. because of desertion)
* pending the outcome of an investigation by the poor-law union into the legal place of settlement
* pending the resolution of a legal dispute between two poor-law unions over place of settlement
* awaiting preparation of a magistrate's removal order to move them to the appropriate union
* prior agreement by one union to pay the relevant costs to the other, thus avoiding physical removal
* too ill to be physically removed, so being held under a suspended order until sufficiently recovered
* pending some other sort of investigation, e.g. medical assessment, or mental-health assessment before admission to an asylum (14-day limit on this)
No doubt there would be other circumstances too.
Do you want to post details of the couple that you've found?