It seems that when ever Im going up a scale or run I alt pick it but coming back down the exact same lick I'll econo pick it. Is this a bad habbit that I should try to break? I know half of the answers are going to be "You should be able to do it both ways..." but will this hurt me in the long run?
Proghead and Proud
as long as its not causing u any problems like you play slower coming back or going down id say no
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I would try to break the habit. It will put that type of pattern into your muscle memory which may make things difficult in the future with certain pieces. Practice doing it both ways individually very very slowly and then gradually increasing.
i used to eco picking everything i played, now i only use alt pick ( exept for sweeps ) and i feel more consistency in my picking
i scream for ice cream
I don't like to do the either or I just pick how it feels comfortable. Nothing wrong with Economy picking...most tend to think it is harder than alt picking... I think its easier...but thats just my opinion
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I also think you should break that habbit. It may seem that it doesn't affect your playing, but it means something is wrong.

If I were you, I'd try to practice both techniques, but wouldn't mix them while practicing.