At the professional level, most Assistant Referees carry matching flags. However, many basic starter sets for new referees have one orange and one yellow flag. The intended purpose of this is not clear, but two possibilities come to mind. First, one color might have been used to denote the "senior (or first) assistant referee". Another possibility is that each AR is expected to have the pair, and the referee could choose, based on lighting conditions or personal preference, which color the ARs should use.
Most flags have both orange and yellow components on the same flag, and come in matching pairs. The unmatched pair is still sold in starter kits today, but are rarely seen above the youth and recreational levels.
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