There were a couple of issues we encountered over the years using FluentMigrator.
The ordering of Migrations in FM depended on an Attribute on the Migration class, taking a long to use when sorting. By convention, this was to represent a timestamp at a particular precision (yyyyMMddhhmm), but that wasn't always followed. Additionally, we got out of sync on the precision to use. Since this was represented as a long, 20150102120059 would be sorted after 201501011200, which wasn't the intent.