Ligatures is the name for two lettered that join or connect. This should help
http://en.wikipedia.org/wiki/Ligature_(typography)
Alternates are differing letters. For example, a typeface may have alternate 'a' which looks subtly different to the standard. They are normally accessed from the 'glyth' menu and replace characters where a letter might look a bit wrong or something?
You should find in your font options that you can turn on/off the ligatures.