Is it wise (and common) to publish in a peer-reviewed journal without an impact factor to prevent impairement of one's own mean impact factor? I recently found out that a team of colleagues published in a journal without impact factor, though peer-reviewed. According to my supervisor this happens sometimes when the study cannot be published in a top journal, and then it could be better to do so than publish in a low profile journal whose impact factor would drag down the mean impact factor of the papers published by that team. 

Is this common? If so, which elements can specifically drive a research team to choose this option?
This reasoning is Wrong and Bad in several ways.


First, computing "mean impact factor" for a person or group is insane and should be resisted at all costs.  Even amongst IF-crazy groups, the metric is generally how many high-IF publications have been obtained (ignoring low-IF publications), not the fraction of high-IF publications.
Second, even if you're going to commit yourself to such insanity, the reasonable mathematical interpretation of "no impact factor" is "IF = 0", not "omit from data."  Thus, if you're using this crazy statistic, it should be worse to publish in a no-IF venue.
Finally, a journal with no IF generally falls into one of two categories: either it is good but very new (or just not yet covered by ISI), in which case it will likely have an IF in a couple of years and the strategy will be undone, or else is it complete trash and likely predatory, in which case it will be a worse stain on your record than a moderate-IF publication, even amongst the most IF-crazy communities.


My only possible conclusions are that either:


your supervisor is seriously distorted in their thinking, or
your supervisor is lying to you out of embarrassment to cover the fact that they published (intentionally or accidentally) in a trash/predatory journal.