Your mortgage interest, property taxes, charity donations and state income taxes are deducted on schedule A, not schedule C.
You need to review your past tax returns. You might want professional help. You might also want to amend for additional refunds, in which case you need to do that by April 15, 2019 to amend for 2015. (For 2016 and 2017 the deadline is next year.)
This is what is supposed to happen: You report your gross self-employment income on schedule C, along with ordinary and necessary business expenses. This calculates a net income (profit). Your net income flows to schedule SE for self-employment tax (about 15% of self-employment income). The net income from business also flows to form 1040 where it is combined with other income such as wages and investments, then your personal deductions and credits are taken into account, and your income tax is determined. Your income tax and self-employment tax are added together and that is your final tax due. If you paid more into the system from withholding and extra payments than you owe, you get a refund. If you under-paid, you owe a final payment.
The expenses from your W-2 job are entered on form 2106 (for tax years 2017 and earlier) and that goes to schedule A subject to the 2% rule; your expenses for the self-employment goes on schedule C and is not limited.
Now, let me describe two possible scenarios of how you might have reported your side income.
If you reported it as "Other income" or hobby income, it would go on line 21 of form 1040. You do not have a schedule C. You deducted your expenses on form 2106. This is incorrect, because you did not pay the self-employment tax. By not paying SE tax, you are cheating on your taxes, and you are also depriving yourself of retirement and disability credits in the social security system. You might not get caught, but the IRS has 6 years to audit you. If you amend and pay up, you will owe late payment penalties and interest, although you can apply for a waiver of the penalties.
If you reported it as self-employment income and you do have a schedule C, but you only deducted expenses on form 2106 and not schedule C, then you over-paid your self-employment taxes. Deducting expenses on schedule C reduces both your income subject to income tax and also your income subject to SE tax. If you did not allocate your expenses between form 2106 and schedule C, then you probably overpaid your SE tax. Taking some expenses off form 2106 will increase your W-2 taxable income but will decrease both your schedule C taxable income and your SE income, so a net positive gain for you. You can amend back to 2015 if you get it in by April 15, and assuming you still have records that can determine which expenses were allocated to which jobs.
And as I mentioned before, if you and your spouse both do side gigs, you need separate Schedule Cs in each of your names. If you work together and get one check, split it and split your expenses. You need to be keeping really good records of course.
