Since tha bacpac file is not transactional, so when the bacpac is being generated, writing new rows to your target database will end up corrupting the index. The database should either have no other users, or it should be copied and a bacpac should be made from the copy.
1. Copy the target database (the database will take some time to copy), The following operation will create a full transactional copy:
CREATE DATABASE <name> AS COPY OF <original_name>
2. Find the status of your copy operation:
SELECT * FROM sys.dm_database_copies
3. Generate a bacpac file on the copied database, which isn't being used by anyone
4. Delete the copied database, and you'll have a working bacpac file
You can see the progress of the copy in their portal.