The Gemara Yoma quoted below enumerates five words in verses of the Pentateuque for which it's not clear, according to Issi Ben Yehuda if they are attached to the previous words or to the next words.
Yoma 52ab (Translation from Soncino).
Surely it was taught: Issi Ben Judah said: There are five verses in the Torah [the grammatical construction of] which is undecided:lifted up',(1) 'like almond-blossoms';,(2) 'tomorrow',(3) 'cursed'(4) and 'rise up'.(5)
(1) Gen. IV, 7: The meaning could be: If thou doest well (good!) - but thou must bear the sin, if thou doest not well; or the usual interpretation: If thou doest well, there will be forgiving (or lifting up of face) ; and if thou doest not well, sin coucheth at the door.
(2) Ex. XXV, 33: Three cups, made like almond-blossoms in one branch, a knop and a flower, or: Three cups, like almond-blossoms . . a knop and a flower.
(3) Ex. XVII, 9: Go out and fight with Amalek tomorrow; I will stand on the top of the hill, etc.
(4) Gen. XLIX, 6, 7: And in their self-will they houghed oxen. Cursed be their anger, for it was fierce. Or: And in their self-will they houghed the cursed oxen. Their anger was fierce. (The cursed oxen would thus be an uncomplimentary reference to Shechem, a descendant of Canaan cursed in Gen. IX, 25) .
(5) Deut. XXXI, 16: Behold thou art about to sleep with thy fathers; and (this people) will rise up. Or: Behold thou art about to sleep with thy fathers and (wilt in future) rise up. This people will go astray after the foreign gods. - Tosaf. s.v. endeavours to account for the curious order of the sentences quoted.
But according to the Masoret, for almost each case the link to the previous word is obvious, e.g. the previous word is followed by a Sof Pasuk for the word"cursed".
So I don't understand why Issi Ben Yehuda didn't simply follow the Masoret. From Rashi in a next passage, it seems that there is a doubt in a verse in which Rav Chisda has a similar doubt, the question is if we have an Etnachta or a Geresh. There is no a sure Masora?
Nafka Minah. Ama Traksin following our Masorah needs to be Kodesh Hakkodadhim, and we are poskim following the doubt of Yosef Ish Hutsal (regarding a verse in Melachim, addressing the status of Ama Traksin) that it's a doubt, see Rambam Bet Habechira 4.2. So, it's seems that our Masorah doesn't help Halachically.