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Since you were working as an independent contractor for a company, it is proper for that company to include all the money they paid you on the Form 1099-MISC. That does not mean that you will be responsible for paying taxes on that total amount though.
When you work on your Schedule C to report your income and expenses as an independent contractor, you will report the full amount as income when you enter the Form 1099-MISC. Then, you will include the amounts that were reimbursed to you as an expense. That way, you will not be paying tax on the reimbursement because it will be subtracted from the income.
You could enter it in the Less Common Expenses section, using the Other Miscellaneous Expenses category. Doing so will allow you to enter your own description for the expense (such as reimbursement for supplies) so that you can categorize it any way that makes sense to you.
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