Help with unexpected results

I ran a comparison between 2 large databases. The databases for the most part are similar. I would expect to find a few differences. The results of the comparison show that one database is missing all the tables and stored procedures from the other database. The compare tool found a few identical objects (44) and a few objects with differences (6). The other 1000+ objects are said to be missing from the other database. Is there something obvious I could look at to correct this?

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