When tables have different number of indexes the compare will show differences when in reality the indexes are the same, just not aligned.
A table on server 1 has 2 indexes. The same table on server 2 has 4 indexes. Depending on the order that the script generates the DDL the compare might show all 4 indexes as different/new where it should show 2 as the same and 2 new.
Rick Thorington commented
Why is this still a problem in 2020?
Please fix sorting/alignment!
SQL Compare 18.104.22.16846
Daniel White commented
This is a general problem not confined to just indexes. For another example, if two stored procedures are the same except for spacing and the placement of the line breaks, the differences pane highlights much code that is not actually different.
Dan Tibbs commented
Yeah, this is a pain. I always end up having to specify only the table containing the index differences and generating a deployment script to confirm what will happen if deployed in regard to the indexes. In many cases several items are highlighted in the difference pane, with crazy alignment that is hard to follow. Upon generating the script I can see what is going to happen and it doesn't seem to match what is displayed in the difference pane...
Alex Fekken commented
I have seen similar behaviour.