1. When you generate a LT report with following filters :

In the above screen shot , the completed status is unchecked.

2. Upon downloading the report , the courses which are completed also populated.

Steps to resolve :

1. As per design, the filter is applied only at the LO level (higher LO) and the child LO can be in any any Status including completed as per the above scenario.
2. Check wheather those courses are part of Learning Program/path or the certification which the user is enrolled into.
3. Check the status of those higher Lo’s which should be Inprogress as per the filter selected above.
4. The higher LO which are Lps and certifications will be Inprogress state and the child Lo’s might have been in completed status.
5. Hence those Child Lo’s which are completed gets populated in report as the Higher Lo’s are still in Inprogress state