I think I remember that, in disputes between Rabbi Meir and Rabbi Yehuda, we follow Rabbi Yehuda except in two occasions. Is this correct and where are these two instances?
Ordinarily the halachah is not in accordance with R. Meir since, as explained in BT (Eru. 13b), “his colleagues were unable to ascertain the profundity of his opinion” (Trans., and others hereon, from Sefaria). Indeed, when R. Meir is in disagreement with, for example, R. Yehudah the halachah is in accordance with the latter (cf. @mbloch’s answer). However, we also have on record that “Shmuel said that the halakha is in accordance with the opinion of Rabbi Meir with regard to all of his decrees” (BT Ket. 57a, cf. also Eru. 47a). Upon consulting a few cases it appears that the halachah follows R. Meir in more than two occasions:
The following things are forbidden to be sold to idolaters... Rabbi Meir says: also a “good-palm”, hazab and niklivas are forbidden to be sold to idolaters (Mishnah AZ 1:5)
It is taught in a baraita: Rabbi Meir says: In the case of anyone who reduces the amount of the marriage contract to lower than two hundred dinars for a virgin or one hundred dinars for a widow, this marriage amounts to licentious sexual intercourse... (BT Ket. 56b)
Based on this baraita, a particular case of a lost ketubah (ibid 57a) was ruled in accordance with R. Meir as his reasoning was enacted as a gezeira (decree).
If a man deposited a sum of money with an agent for his daugher, and [after she was betrothed] she says, “I trust my husband”, the trustee must act in accordance with the condition of his trust, the words of Rabbi Meir; Rabbi Yosei says... (Mishnah Ket. 6:7)
If one slaughtered the first born and then showed its blemish [to an expert]:Rabbi Judah permits, But Rabbi Meir says: since it was not slaughtered by the instructions of the expert, it is forbidden. (Mishnah Bekh. 4:3)
The gemara clarifies that R. Meir’s ruling is a matter of penalty. Rambam (MT, Bekh. 3:4), and others - see KM, seemingly equate this to a gezierah and therefore rule in accordance with R. Meir whereas Tosafos (Bekh. 28a and Betz. 27a), following R. Ahai Gaon, differentiate between a penalty (קנס) and decree (גזירה) with regard to ruling like R. Meir.
You are correct that the gemara in Eruvin 46b writes that
Rabbi Ya’akov bar Idi said that Rabbi Yoḥanan said: In the case of a dispute between Rabbi Meir and Rabbi Yehuda, the halakha is in accordance with the opinion of Rabbi Yehuda
Where Rabbi Meir is named in as a source, and his decision is disputed, either by Rabbi Yehuda, Rabbi Yose, Rabbi Shimon or Rabbi Eliezer ben Yaacov, the halacha is like his opponent
@Oliver in his comment to your question above has already mentioned a number of exceptions; I will let him write them up in an answer.