Columns are marked as different but they seem to be identical! In some cases you may see a table pair marked as different and when you look at the "Schema Differences" tab on the bottom you may notices that one or more columns have been highlighted as being different but there is no visible difference on the script! In these cases you will need to dig deeper to find out why those columns are marked as different. To do that expand the table on the top section and then click on the column you are interested on - on the bottom section of the screen you will see the script for that particular column with the different section highlighted. This difference will be visible on the table script as well however it is a lot easier to "spot" on the column script. Differences on default constraints, check constraints, default bindings, rule bindings, or extended properties can cause the columns to be flagged as different.
Columns are different but are not marked as such! The highlighting of the differences on the script of an object is controlled by the comparison engine so if the comparison engine marks two objects as equal then nothing will be highlighted on the scripts of those objects even though there might be visible differences on the script. Why does this happen? The answer lies in the comparison options - there are a few options related to collation, nullability, replication, identity etc. that affect the column comparison. So if you have for example chosen to ignore the column collation then even though the column on the left might have a different collation from that on the right the columns will be marked as equal and therefore the collation difference on the script will not be highlighted.