There are several issues here.
First of all, what do you mean "my taxes indicate that I am single"? As long as you were married on December 31 of a year, you can NEVER file as single on your taxes for that tax year. Someone who is married can file as Married Filing Jointly or Married Filing Separately (or in rare cases Head of Household). This has nothing to do with anybody's immigration status or anything. It's just wrong tax filing. If you filed your taxes wrong, you need to fix it, regardless of whether you are applying for naturalization.
They will not deny your naturalization because of your wife's immigration status.
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