One can find a list of some words that R’ Yaakov analyses in the index of the expanded edition of Emet L’ Yaakov on Chumash. For now I will focus on one significant example.
Shabbos 33b: (בראשית לג) ויחן את פני העיר אמר רב מטבע תיקן להם ושמואל אמר שווקים תיקן להם ור' יוחנן אמר מרחצאות תיקן להם
Rashi finding it difficult to relate the word Tikkun to the word Va’Yichan suggests that the Gemara refers to the next Passuk (Did Rashi have a different Taamei Ha’Mikra here?)
וַיִּקֶן אֶת-חֶלְקַת הַשָּׂדֶהֹ - VaYikan according to Rashi is related to the word Tikkun.
The Maharsha comments that “this is difficult since we only find the term Tikkun in Kohelet [!!!] and never without the Tav which is a root letter.”
R’ Yaakov comments on this that we do in fact find letters in Rabbinic Hebrew with a Tav that lack a Tav in Tenach. He cites as in example the word Terumah which in the Chumash is written וירם without the Tav. [1a]
I am exceedingly surprised that both the Maharsha and R’ Yaakov noted the frequent use of Mishnaic Hebrew in Kohelet and passed over it without comment. 
[1a] I recall the term Terumah being used as a prime example of the differences between Biblical and Rabbinic Hebrew in one of the "Wissenschaft das Jedentums" works but I have forgotten where I saw this. Can anyone recall what this might have been?
See the introduction to the standard Mishnayot on the nature of Mishnaic Hebrew and in the footnote there – רק בקהלת והטעם ידוע למשכילי עם . Surprisingly this disgustingly snide comment has not been removed from the new Zecher Chanoch edition.
See also R’ Chaim Dov Rabinowitz in his interesting From Nechemia to the Present: A History.. In one of the discussions there he writes how upset he is that this article was included in the Mishnayos. R’ Rabinowitz’s writes that Tenach uses a higher Hebrew and therefore does not contain all of the words used in daily life. This according to his view, accounts for all the difference between Biblical .and Rabbinic Hebrew. That R’ Rabinowitz was aware of at least some of the issues of Bibical criticism is obvious from his introduction to Daat Soferim - Isaiah and various other apologetics scattered throughout his work. See also the Radziner’s scathing review in HaDarom complaining (among other things) of the apologetic tendency in the Daat Soferim.