If you wife's HOR is Connecticut, as a Military Spouse you can elect CT as your Resident state also.
Click this link for more info on Military Spouses.
Since you file separate state returns, and your wife is filing correctly as a 'Non-Resident' to CT, if you also file as a CT Non-Resident, you will still need to file a Resident return to Maryland, as your income is still reported there.
If you file as a CT Resident, you would need to file a Non-Resident return to MD, as your income was earned there. Sounds like you may be better off the way you've been doing it!
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