Taxable income is the fees and bonuses. Reimbursements are not taxable. You are required to claim your fees and bonuses on your Schedule C of your tax return whether you receive a 1099 for them or not. Rarely is a 1099 going to match your records, not from any mistake on anyone's part, but simply from how the accounting is done.
Lets say you worked a lot for a company during the year and did 4 jobs at $20 each for them in December--12/1, 12/5, 12/15 and 12/30.
The company issues you a check on 12/16 for the first two jobs which you receive on 12/20 and a check on 12/30 for the third job that you receive 1/5 and a check on 1/20 for the fourth job, which obviously you will receive in late January.
The 1099 will include the first 3 jobs because the company sent checks out the door to pay them before the end of December.
As a cash taxpayer you would only claim 2 of the jobs because that was what YOU had received payment for by the end of December.
As an accrual taxpayer you would claim all 4 of the jobs because it was what you had EARNED prior to the end of December.