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It is perfectly normal to have multiple formats against a given book record. In practise that is probably what most people prefer to end up with so that Calibre can select the most appropriate format for any given reading device.
When adding new books, if Calibre finds multiple books with the same author/title it warns you about duplicates. There is a 'tweak' available to control what should be done in such situations - add them to existing records or add them as new records. You can get false positives so you do need to exercise a little caution in letting Calibre automatically merge different formats onto the same library record. Also there are scenarios where you may genuinely want multiple entries for the same book (e.g. different editions) which is one of the reasons Calibre allows duplicates to be stored.
You can also select multiple entries after they have been added and use the Calibre 'merge' option on the right-click menu to merge them into a single record as long as you are sure that they are really the same book.
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