First of all, if you are married, you cannot file as "Single" filing status. You can only file as "Married Filing Separately" (on the 1040NR this is called "Other married nonresident alien"; nonresident aliens cannot file as "Married Filing Jointly", so this is the only married option). Is that what you mean they processed it as?
The fact that you tried to put $6300 in Line 38 (itemized deductions) indicates that you were trying to claim the standard deduction, which is available to students under the US-India tax treaty. Is that what you were trying to do? If so, did you write "Standard Deduction Allowed Under U.S.-India Income Tax Treaty" on the dotted line on line 38, as instructed in Worksheet 5-1 in Publication 519?
Under the US-India tax treaty, students can claim an exemption for their spouse and dependents, as long as those spouse/dependents are not filing a tax return and cannot be claimed by someone else. Is that why your wife was applying for an ITIN? According to Publication 519, if you are doing this, you are supposed to list your spouse and dependents under Line 7c (dependents). Your spouse is not your dependent, but for the purposes of using this US-India tax treaty provision, you are supposed to list her under "dependents", and not check "spouse". Is that how you filled it out?