Officially, the German club had received 5,000 tickets.
For the big matches in the future, the tickets will have a personal connection for easier tracking.
The club will also try to gain better control over the resale of tickets to outside agencies.
The club now apologizes to the fans who were disturbed by the large number of German fans who took over their own home castle.
According to the AP, there were over 30,000 German fans in the arena, where the official audience figure was 79,468.
Exactly how many German fans there were in the arena could not be determined.
Many Spain-based Germans were also in the arena.
Not everyone flew in from Frankfurt or other German cities.
"We can only make estimates"
- We do not know for sure how many tickets were used.
We can only make estimates.
We do not want to put anyone there, but we are very disappointed, says President Joan Laporta.
The team lost to Frankfurt by 2-3 and left the Europa League with 3-4 in total.
Fans protested during Monday's league match against bottom team Cadiz and left a section empty in the huge arena.
It was a new loss, 0-1, and not since 2003 has Barcelona lost two straight games.
On Friday, Barcelona's ladies will play with Fridolina Rolfö as key player in the first semi-final against Wolfsburg in the Champions League and then the new ticket routines will be in place.
When Barcelona met Real Madrid in the quarter-finals three weeks ago, an audience record was set for a global club team match with 9,1553 spectators at the Camp Nou.