One of the few Biblical arguments Catholics make for their interpretation of the Eucharist is that after Jesus told the disciples that they must eat His flesh and drink His blood in order to have eternal life, many of them were offended and left, saying "This saying is hard; who can accept it?" (John 6:60).
The first problem with this particular line of reasoning is that it's disputable exactly how connected John 6 is with the Lord's Supper in the first place. Though the metaphor is similar, this scenario occurred before the institution of the Lord's Supper (Matthew 26:17-30; Mark 14:14-26; Luke 22:7-20 cf. 1 Corinthians 11:17-34), and has no direct references to it. Furthermore, Jesus actually explains His meaning even within John 6, with the described purpose being explicitly different. In John 6:35-37, He explains that He is talking about coming to, and believing in Him, as the criteria for salvation, whereas the purpose of the Lord's Supper is not stated as being salvific, but rather "do this in remembrance of me". Thus, one can reasonably conclude that John 6 isn't even Eucharistic.
But why did the disciples leave if Jesus wasn't speaking literally? This is actually the explicit purpose for why Jesus so rarely spoke plainly. In Matthew 13:10-17 and 13:33-35, Jesus cites two Old Testament Scriptures, namely Isaiah 6:9-10, and Psalm 78:2, to tell His disciples that, while they had been given understanding, the Jewish people were stubborn, both historically and in the present, and thus Isaiah prophesied Jesus would speak to them in parables so "...seeing they do not see, and hearing they do not hear, nor do they understand". But later on, in John 16:25-33 (notice, after the events in John 6), Jesus promises He would soon cease to use figures of speech. In other words, up until this point, He had been. This should be obvious from virtually everything else He said up until this point, but you also cannot cease to do something you weren't doing in the first place. Furthermore, in verse 29, the disciples' reaction was basically "finally! Now we understand!" Even they were amazed when He spoke to them plainly, using no figures of speech, showing that even they had trouble understanding Him up until now.
Ultimately, God understands His purpose, and how to achieve it. This includes using strange phraseology, such as "I am the door of the sheep" (John 10:7), or "I am the true vine" (John 15:1-4), and letting stubborn and rebellious people abandon Him for it. You will find that there are very many strange figures of speech Jesus uses, but for some odd reason, only one of them is insisted upon as literal. Yet, such an interpretation is contrary to both the Jewish religion (the Law forbids consuming blood, and doesn't look too favorably upon consuming human flesh, either), and the Christian religion (Christ's two natures do not overlap, as even the Council of Chalcedon acknowledged, meaning His body cannot be omnipresent).
Therefore, we are compelled by Scripture and reason to reject the Catholic interpretation of the Eucharist, regardless of what a few false disciples thought of Him. It doesn't even make sense to suggest they necessarily understood Him to be speaking literally. That wasn't what they said. Even if it genuinely was what they believed, they fled from the one and only Son of God because they didn't like His teachings, so they're hardly ideal theologians! Why would we trust them to interpret the word of God if they walk away from Him when He speaks it to them with His own mouth? Far better to trust the Scriptures themselves, which plainly tell us that the bread is bread (Matthew 26:26; Mark 14:22; Luke 22:19), the wine is the fruit of the vine (Matthew 26:29; Mark 14:25; Luke 22:18), and the purpose of the Lord's Supper is in remembrance of Christ (Luke 22:19; 1 Corinthians 11:24-25), and proclaim His death until He comes (1 Corinthians 11:26). If you trust the apparent interpretations of the fleeing disciples over the explicit teachings of Scripture, you have a lot more in common with the fleeing disciples.