This issue has been puzzling commentators for thousands of years, if we take it broadly as "how many eyes did Homer think Polyphemus had, and why?"
The Greek text of Odyssey 9.389 uses the plural word "ὀφρύας" for the brows, and indeed "βλέφαρ" for the lids, although we could interpret that as meaning the upper and lower lids of the single eye. In the rest of the story, Homer does not say outright that Polyphemus had one eye, although since Odysseus managed to blind him outright by destroying one eye, it's a natural conclusion. Translators of the Odyssey have probably tended to keep the problematic plural, since it is after all part of the received Greek text. In this way, they are preserving its oddity and ambiguity for the English-language readers.
Subsequent authors who adapted this story, such as Euripides, have been more consistent in presenting him as one-eyed. The same is true of the account of the cyclopes by Hesiod - thought to be a contemporary of Homer - in his Theogony.
Homer's use was noted in the scholia, which are critical annotations of various origins preserved in the manuscript traditions. We do not have a lot of information about which bits of commentary came from which authors, but some of them certainly date from the time of the classical Homeric editors such as Aristarchus. One such annotation to the lines in question reads:
According to Homer, the Cyclops was not one-eyed as Hesiod says. Indeed he says 'all around his eyebrows and eyelids' and not like Theocritus 'for a wide eyebrow stretches over my entire forehead'. Thus, according to Homer he was one-eyed, as one of his eyes had been blinded before.
(Quoted from Hesiod's Verbal Craft: Studies in Hesiod's Conception of Language and Its Ancient Reception, Athanassios Vergados (OUP, 2020), p303. The reference to Theocritus is for his Idyll 11.)
In this reading, Polyphemus was originally two-eyed, but lost one of them in some incident prior to Odysseus' arrival. This notion relates to a riddle in Aristotle's lost work Homeric Problems, a collection of questions and answers about puzzling aspects of the works. Surviving fragments include the problem of why Polyphemus is said to be a cyclops, when neither of his parents - the god Poseidon and the sea-nymph Thoosa - were cyclopes. The answer is another puzzle: that this is no less likely than the winged horse Pegasus being born from the union of Poseidon and Medusa, which is to say that these stories come from mythology and cannot be expected to be squared with our ordinary knowledge of biology. It can be "mythologically true" that the character has one eye, even without an obvious reason - it's an attribute of the myth that we expect. The inferred prior loss of the other eye is a way to reconcile the mythological requirement (we very much expect Polyphemus to have one eye only) with the textual context (his cited parentage and the plural brows). (See Robert Mayhew's Aristotle's Lost Homeric Problems (OUP, 2019) pp14-15.)
In any event, this sort of reasoning is typical of ancient critics who wanted to find rational excuses for apparent mistakes in Homer. Another response would be to say that this is a genuine slip; "even Homer sometimes nods", as Horace said in Ars Poetica (c. 19 BC). A more modern approach would be to recognize that what we have today as "Homer's Odyssey" is a distillation of several poetic sources, not necessarily all composed by the same person, and edited to some unknown extent by the Alexandrine grammarians by the time the text made its way to us. The story might therefore preserve several different traditions about what sort of creature Polyphemus was. For example, his connection to Poseidon makes sense in the overall story of the Odysseus' relationship to the gods, but might not be original to the tale of how a clever hero poked out a giant's eye. It might not be meaningful to ask whether "Homer" understood the character to have one eye or two, if this episode represents a traditional story about Odysseus outwitting a cyclops, adapted to fit within the epic by adding plot connections for Odysseus angering Poseidon by maiming his son.