The instalment payments you make to CRA are based on the "calendar year". So if any of those instalment payments were made in 2019, they may not be showing as available to apply to your 2018 tax year.
Another thing that does happen is when you made an instalment payment, your bank may have "misdirected" it and applied it to another CRA account (such as GST or Payroll if registered). If you have a CRA My Account, you can log in there and look at a "Statement of Account" and see if all your payments have been posted. Then give CRA a call and inquire about the status of any payments you may have made.
CRA General Enquiries: 1-800-959-8281