Yes, that will happen. The phone will have contacts from 'phone', sim and your gmail account. If you do not want to bother to delete them, simply select display options and select which ones you wish to see.
However, there does appear to be some glitch, since if only 29 were showing in your gmail a/c then only 29 should be linked/duplicated.
I would delete the 'phone' contacts and use gmail contacts - it has many advantages - you are always backed up, you can manage contact groups easily, you can find duplicates with part info in each and merge them, etc. If as with all of us, there may be large number of e-mail contacts who one does not call, then again in display options (or maybe in google a/c settings) you can choose to display only contacts with phone numbers.
In the alternative you would require to use something like MyphoneExplorer on PC and a contacts app to manage the 'phone' contacts.