Well I think its because the license where issued in a foreign country and as a government Qatar has to recognize the laws of other countries but once a matter is relocated to another country then they will have to fall under its authority.

When accepting the marriage license it was probably for visa and emigration issues which is delt with in a specific department.

Now when they broke the law of the land by kissing in public and showing no respect for the morals and culture of this country and people then the issue is transferred to a totally different department which is the ministry of Justice.

As a court it has a set of laws and this law doesn't recognize the marriage. Its legal for a nonemuslim to have a girlfriend and such and at times of dispute they are delt with as such.

Now its a fallacy that a muslim woman is married to a non muslim man. So simply its rejected. They might be legaly married in some other country and immigration wise they are treated as a married couple but legal wise its ether adultry or she is not a muslim.

An example is a gay couple. they might be legally married somewhere in the world. but they will not be tolerated here.

that said i presume that it was an error by immigration officials to accept the license.

BUT..the main issue is..Married or not Married....its still against the law to engage in indecent acts in public in Qatar whom ever you are.
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Seriously people if you do not like our way of life then you can leave if you cant tolerate it.
To you your way and to us ours.