The single biggest issue with protein contamination using this method of purification is ensuring complete cellular lysis.  If this and the subsequent wash steps have been performed adequately eluting your sample in a smaller volume, though inevitably concentrating any contaminating proteins, shouldn't be a problem.  When eluting with a smaller than recommended volume I always 1) let the eluent sit on the column for about 5 min before spinning and 2) re-apply the elutent to the column a second time.