Thank you for all the information.
But it turns out that my problem was caused by something else.

I have a table in the report. The table is generated by a Velocity Template Language template.
In the table, there is a cell that has multiple entries.
The cell used a bullet list. The list had three entries. This is why three numbers were inserted, causing the TOC to skip from 2 to 5.
When I removed the bullet list format the numbering was corrected.