Without some sample data this is hard to debug.
If you're looking at this in PowerQuery, please keep in mind that only the first 1000 rows are being loaded per time. If your combined dataset is larger than that, then there's a chance that you're not seeing the full results before filtering (and again, the rows that you see in PowerQuery might again look slightly different when you load them into PowerBI).
Also, with inner joins, check that the column that you are joining on is UNIQUE. If there is a duplicate in either of the original datasets, then your joined table will also have a duplicate row. It's strange to me that the number of rows increases after filtering, rather than joining / expanding the columns, so maybe you need to take another look at your source tables. Good luck.
