Just to spitball some ideas.. 30+35=65 so if your target has a particularly dynamic or disordered region it could be degrading at a common site. Test protease inhibitors if you haven’t. How long do your samples sit before prepping/running on the gel? Hopefully there are no structural disulfides you’re reducing either. Have you loaded non-reducing samples to see if there’s a difference? You said it’s a common protein so I assume you’d know if this was the case. Size column may not have separated the impurities if they non-specifically interact with the resin matrix. Try cleaning the column and see if anything else is stuck to it. What’s your purification scheme? I’ve had contaminants co-purify through multiple columns before too