The clearest scientific error in the Quran is its claim that the Sun sets in a spring of muddy water.
18:86 - Hatta itha balagha maghriba alshshamsi wajadaha taghrubu fee AAaynin hami-atin wawajada AAindaha qawman qulna ya tha alqarnayni imma an tuAAaththiba wa-imma an tattakhitha feehim husnan.
18:86 - Till, when he reached the setting-place of the sun, he found it setting in a muddy spring, and found a people thereabout. We said: O Dhu'l-Qarneyn! Either punish or show them kindness.
This verse is alone enough to show that the Quran is falsehood. According to the verse, the Sun has a setting place on Earth that we can reach, where it was found to set in a "muddy spring"
There are two defenses that are offered by Islamic apologists to this:
1). That the verse is talking about reaching the time of sunset - clearly refuted by looking at the context and wording of the verse - "till when he reached the setting time of the sun" has no meaning if the verse meant setting time of sun.
2). That the verse is talking about reaching the westernmost point that he can reach in the direction of sunset - again refuted by the context and wording - "till when he reached the west, he found it setting" - here "it" has no meaning if the words maghriba alshshamsi meant west because the word sun has not even been used to know what "it" refers to.
Besides, this blatant error is confirmed in the authentic (Sahih) hadiths.
Sunan Abu-Dawud 4002 (Sahih) - Narrated Abu Dharr: I was sitting behind the Messenger of Allah who was riding a donkey while the sun was setting. He asked: Do you know where this sets? I replied: Allah and his Apostle know best. He said: It sets in a spring of warm water (Hamiyah).
Every single Tafsir for the first 440 years after Muhammad's death (19 Tafsirs in this period) supported this claim:
Tafsir Mujahid (104 After Hijra), Tafsir Ghareeb al-Quran (120 AH), Muqatil bin Sulaiman (150 AH), Tafsir Sufyan al-Thawri (161 AH), Tafsir AbdulRazaq al-Sanaani (211 AH), Tafsir al-Quran - Al-Tustari (283 AH), Tafsir al-Hibri (286 AH), Tafsir Furat al-Kufi (~300 AH), Tafsir al-Hiwari (~300 AH), Tafsir al-Nisa'i (303 AH), Tafsir al-Tabari (310 AH), Tafsir Nazhat al-Quloub (330 AH), Ta'wilat Ahlul Sunnah (333 AH), Tafsir Bahr el-uloum (375 AH), Tafsir IbnAbi Zamanayn (399 AH), Tafsir Ali Ibrahim al-Qimmi (~400 AH), Haqa'iq al-Tafsir - Al-Silmi (412 AH), Tafsir al-Kashf wal bayan (427 AH), AlHidaya ila bulugh alNihaya (437 AH) - all of them clearly stated that Sun literally sets in a spring of water.
It was only Tafsir Al-Mawirdi written 450 AH which first started suggesting that it could be talking about it being an illusion - as an alternate theory - it didn't dismiss the main theory of Sun setting on a spring. These interpretations developed as a result of scientific knowledge about Sun's size rather than an objective translation of the verse.
And besides, even if we ignore all of this and buy the unlikely claim that somehow Dhul-Qarnain had an illusion of sun setting in a spring, lets take a look at the picture of the largest spring in the world - the Frying Pan Lake in New Zealand:
Clearly, even the largest spring in the world is not large enough to cause this illusion. Humans can clearly see far enough by simply standing up.
Conclusion: This is a clear scientific error in the Quran and the evidence that points to this error is overwhelming not only from the Quran itself, but from the authentic hadiths and earliest tafsirs. To pretend that there is nothing wrong in this passage would be delusional at best.