I'm also a membership clerk. I'm assuming you're using LCR to look at the records. In LCR, the view you have of each individual membership record has a 'Household' tab and a 'Family' tab.
The 'Family' tab is where family (marriage, parent-child, etc.) relationships are shown. In the 'Family' tab, each spouse should show up as a spouse on each other's record. That link is essentially symmetrical. Family relationships are unchanged by where respective family members live.
The 'Household' tab is basically groupings of people who live together and are treated as one group unit for ministering assignments and similar things. The bluish-background box in the 'Household' tab has a more complete definition.
My guess (and it's just a guess because I cannot see what you see in LCR) is the spouses show up as spouses in the 'Family' tab but are in different households as seen in the 'Household' tab. If that guess is correct, go to the husband's 'Household' tab. If his wife is not listed as being in his household, click on the 'Add Household Members' link/button and follow the steps to add her to his household.
Some of your best sources for information on handling problems like this would include the training materials, your ward clerk, and your stake clerk. Part of the calling of stake clerks is to train the ward clerks and the assistant ward clerks.