nowadays even when you purchase a round-trip using one of the consolidator websites (expedia, travelocity, orbitz, etc) - they now offer many flight combinations & options, with the outbound on one airline and the return on another... it's become relatively common now to fly the equivalent of two 'one-ways'.

So even when you purchase both at once as a 'round trip', when examining the paperwork, technically it's really two one-ways, and it's become common. While I understand there's a 'possibility' for this to raise a flag for some overzealous TSA employee - it's not a HUGE issue to 'worry' about.