Do put all replications in one data dictionary; do not spread replications across multiple data dictionaries that will be sent to one controller. A controller can only run replications from one data dictionary at a time.
Example: If the data dictionary ex1.cdd is deployed to controller 1 and then data dictionary ex2.cdd is deployed to controller 1, the replications in ex1.cdd are removed and the replications in ex2.cdd replace them.
Do check the log files when data is not replicating. Since the replication controller runs as a background service errors there is no user interface to display errors, so they are written to log files. The log files can be found in the folder at the Installation Directory \CONNX32\Replication\log.
Don't modify target data outside of the replication tool. If data on the target database is modified outside of the replication tool, it can cause integrity issues and stop the replication.
Don't deploy the same Data Dictionary to different active controllers. If there are two different controllers modifying data in the same target table, you lose data integrity from the source to the target tables. This will disable the Event Replicator.