Does anyone know if there is a way to constrain a Hex shaft in a Hex bore on parts in an inventor assembly?
I don’t have personal experience in Inventor, but if you can activate the axis of the hex shaft/bore, you can make them coincident/concentric. Then you would make the faces of the hex shaft parallel with one of the faces of the hex bore
The trick with this is to create and axis through the center of the shaft. Use that axis as a constraint instead of the faces of the hex
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Or use ThunderHex, it has cylindrical geometry down the center 
You should be able to make the center axis visible quite easily. One of the origin axes should be straight through the center. After you’ve made them concentric, you can make an angle constraint between one of the faces of the shaft and one of the faces of the bore to stop it from rotating, and then mate/flush constrain one of the ends however you see fit.