The Mishna in Bava Basra (2:10) says: (all translations from Sefaria)
מַרְחִיקִין אֶת הַמִּשְׁרָה מִן הַיָּרָק, וְאֶת הַכְּרֵשִׁין מִן הַבְּצָלִים, וְאֶת הַחַרְדָּל מִן הַדְּבוֹרִים. רַבִּי יוֹסֵי מַתִּיר בַּחַרְדָּל:
A pool for soaking flax must be distanced from vegetables, and leeks from onions, and mustard plant from bees. Rabbi Yose permits mustard plant.
The gemara (Bava Basra 25b) explains:
תנא רבי יוסי מתיר בחרדל שיכול לומר לו עד שאתה אומר לי הרחק חרדלך מן דבוריי הרחק דבורך מן חרדליי שבאות ואוכלות לגלוגי חרדליי:
A Sage taught that Rabbi Yosei permits one not to do so in the case of mustard because he can say to the beekeeper: Before you tell me: Distance your mustard from my bees, I can tell you: Distance your bees from my mustard, as they come and eat my mustard plants.
As far as I can find on the Internet, there is no indication that mustard is actually harmful at all to honey making. As a matter of fact, this website says that it actually makes perfectly fine honey (search for the word "mustard" on the website). It is on the Wikipedia article List of pollen sources, and is for sale on Amazon.
Is this some factual difference from back then, that the mustard was worse for honey? Or is this another example of Chazal possibly being mistaken? Or a case of נשתנה הטבע (the reality has changed)?