Let me narrate my scenario, which is quite similar. I'm a retainer/consultant with a reputed company and submit a monthly consultancy fees bill, getting paid for the same each month. In the same monthly bill, I also claim amounts for some reimbursements like mobile and local conveyance spent on company business. When I get paid, they deduct 10% TDS on the total amount (including fees and reimbursements) and later provide me with a TDS certificate (Form 16A) for the deductions. I had inquired with them, but their finance says it's as per law. In their words: "As per IT Act 1961, they have deducted 10% Flat on all my Claims & Fees."
Let me know if this is correct.
Your case has been treated as payments to "Consultant," deducting TDS @ 10% u/s 194 J as a precaution to avoid penalty & interest for failure of deducting TDS & remitting to the government. However, you can claim a deduction from Business/Profession income for expenses incurred towards travel, etc., as these are supported by bills.