SQL Server INNER REMOTE JOIN returns more rows than INNER JOIN
TOP 100 with no ORDER BY means it is undeterministic which 100 rows from the remote table end up participating in the join. This is execution plan dependant and can vary.

If it is a one to many relationship it may be the case that one batch of 100 rows has more matches on the other side of the join than another different batch of 100 rows.

You should specify an ORDER BY (inside the derived table) on some unique column or combination of columns to ensure deterministic results.