The book of Ezra is the first time we hear of the concept of the "holy seed" being a concept directly tied to bloodline in Tanakh. I don't think it's accidental that this concept is introduced in the very same verses you are asking about:
וּכְכַלּ֣וֹת אֵ֗לֶּה נִגְּשׁ֨וּ אֵלַ֤י הַשָּׂרִים֙ לֵאמֹ֔ר
לֹֽא־נִבְדְּל֞וּ הָעָ֤ם יִשְׂרָאֵל֙ וְהַכֹּהֲנִ֣ים וְהַלְוִיִּ֔ם
מֵעַמֵּ֖י הָאֲרָצ֑וֹת כְּ֠תוֹעֲבֹֽתֵיהֶם לַכְּנַעֲנִ֨י הַחִתִּ֜י
הַפְּרִזִּ֣י הַיְבוּסִ֗י הָֽעַמֹּנִי֙ הַמֹּ֣אָבִ֔י הַמִּצְרִ֖י
- Now when these things were done, the princes drew near
unto me, saying: 'The people of Israel, and the priests and the
Levites, have not separated themselves from the peoples of the lands,
doing according to their abominations, even of the Canaanites, the
Hittites, the Perizzites, the Jebusites, the Ammonites, the Moabites,
the Egyptians, and the Amorites.
כִּֽי־נָשְׂא֣וּ מִבְּנֹֽתֵיהֶ֗ם לָהֶם֙ וְלִבְנֵיהֶ֔ם וְהִתְעָֽרְבוּ֙ זֶ֣רַע הַקֹּ֔דֶשׁ בְּעַמֵּ֖י הָאֲרָצ֑וֹת וְיַ֧ד הַשָּׂרִ֣ים
וְהַסְּגָנִ֗ים הָֽיְתָ֛ה בַּמַּ֥עַל הַזֶּ֖ה רִאשׁוֹנָֽה׃
- For they have taken of their daughters for themselves and for
their sons; so that the holy seed have mingled themselves with the
peoples of the lands; yea, the hand of the princes and rulers hath
been first in this faithlessness.'
I will now give my personal opinion and thus I am the only source. It's my belief that Ezra didn't "notice," or take action sooner because intermarrying the locals had somehow not caused widespread sin and debauchery. We don't get any public complaints in Tanakh of these intermarried exiles offering sacrifices to pagan Gods, or having idols inside their houses, going to "high places," or eating unclean animals, etc. It seems like these "local" wives and husbands though of non Israelite/Judean stock were willing to either practice Judaism on some level, or at least not corrupt their Israelite spouses to idolatry. Therefore Ezra wouldn't necessarily notice things are amiss, because everyone is acting more or less like they should be. It's also likely that the local Samaritan/Ammonite/Egyptian/Hittite looked very similar to a Judean, so it wouldn't be visually obvious that a couple was intermarried.
But then Ezra is "informed," that all these people have intermarried and have "mingled" the holy seed with the peoples of the lands. These informers also say that abominations are happening.... but no evidence is actually presented. So it is my opinion that the issue of intermarriage wasn't necessarily one of paganism, or idolatry, but rather one of "racial purity." Keep in mind that while racial purity may not matter greatly for a common Israelite/Judean, the same can't be said for the priestly class, the levitical class, and potentially for the descendants of Dawid as princes.
This potentially explains why these informers also emphasize that the "The people of Israel, and the priests and the Levites, have not separated themselves from the peoples of the lands...yea, the hand of the princes and rulers hath been first in this faithlessness."
And perhaps this sheds light on why a council needed to be appointed to seek all these intermarriages out, because otherwise these intermarriages might fly under the radar for generations. This would run the risk of destroying the legitimacy of the priesthood, the levites, and the descendents of Dawid within just a few more generations. So if the idea is that racial purity must be maintained for these classes, it's understandable why Ezra needed to be informed, and why he might take so drastic a measure as sending away all the wives and children, even those of normal Israelites/Judeans.
Another answer here makes the argument that it's possible Ezra didn't believe in conversion. This idea has merits worth contemplating as the author points out that Ezra and his court didn't try to convert these foreign spouses, instead insisting that they must all be sent away, without exception. This seems odd when you consider an average Israelite is allowed to marry converts, so why not convert these spouses? My response is: Because maybe it wasn't a question of whether or not Ezra believed in conversion in general, but maybe the question is whether Ezra believed that Priests, Levites, and Princes could marry a convert from Moabites/Hittites/Egyptians/Amorites/Samaritans/etc.
Note: Nothing in my answer is an attempt to extol, justify, or even critique the idea of racial purity. It is my opinion that Ezra and his informers were motivated by racial purity, but I leave it up to you the reader to decide what you think about racial purity as a concept.