Yes, it would - if you are still
in the US and she is visiting you, that alone may raise a red flag because she is married to a US citizen and may try to stay in the US illegally to be with you.
If they start asking questions, normally the first thing they will want to see is evidence of a return ticket - I has been asked twice in the past to show my return ticket when entering the US.
To be safe, she should also bring with her evidence of money to support her trip and evidence of a life to return to in the UK (job etc.) to prove she won't try to stay in the US longer than 90 days.
If you are travelling together in future - both to the US and the UK, you should go through the same immigration line together. This will probably be the USC line when entering the US and the UKC line when entering the UK, but sometimes you may need to ask which line you should go through.
By the way, all of this would also apply to you if you visited her in the UK before applying for your spousal visa. Simply being married to a native citizen gives you no rights to enter the US pr the U.K. at all - if you want rights you need to get the spousal visa first.
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