What are the recorded cases of disqualification in the ancient olympics and what was the reason for each case?
PS: Don't get into the details about the Hellanodikai, I am very well aware of their function.
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Indeed one such incident is well recorded. I quote from Thucydides, Book Five, Chapter 49 and append my own translation. Both my English and Ancient Greek are rusty now...
Ὀλύμπια δ᾽ ἐγένετο τοῦ θέρους τούτου, οἷς Ἀνδροσθένης Ἀρκὰς παγκράτιον τὸ πρῶτον ἐνίκα: καὶ Λακεδαιμόνιοι τοῦ ἱεροῦ ὑπὸ Ἠλείων εἴρχθησαν ὥστε μὴ θύειν μηδ᾽ ἀγωνίζεσθαι, οὐκ ἐκτίνοντες τὴν δίκην αὐτοῖς ἣν ἐν τῷ Ὀλυμπιακῷ νόμῳ Ἠλεῖοι κατεδικάσαντο αὐτῶν φάσκοντες <ἐς > σφᾶς ἐπὶ Φύρκον τε τεῖχος ὅπλα ἐπενεγκεῖν καὶ ἐς Λέπρεον αὐτῶν ὁπλίτας ἐν ταῖς Ὀλυμπιακαῖς σπονδαῖς ἐσπέμψαι. ἡ δὲ καταδίκη δισχίλιαι μναῖ ἦσαν, κατὰ τὸν ὁπλίτην ἕκαστον δύο μναῖ, ὥσπερ ὁ νόμος ἔχει.  Λακεδαιμόνιοι δὲ πρέσβεις πέμψαντες ἀντέλεγον μὴ δικαίως σφῶν καταδεδικάσθαι, λέγοντες μὴ ἐπηγγέλθαι πω ἐς Λακεδαίμονα τὰς σπονδάς, ὅτ᾽ ἐσέπεμψαν τοὺς ὁπλίτας.
My attempt at a translation:
Olympics took place that summer, in which Androsthenes the Arkadian
won the first pankration.1 and the Spartans where banned from the sanctum by the Elians, so as to neither sacrifice, nor compete (in the Games). For they had not fulfilled their punishment, to which they had been condemned by the Elians under Olympic Law, as the Elians charged that they had brought arms to the fortification of Phyrkon and hoplites2 of their own into Lepreon, all at the time of the (Olympic) Truce. The fine amounted to 2000 mnas3 , two per hoplite, as the law provides. But the Spartans, sending ambassadors, maintained they had unjustly been condemned, saying the Truce had not been announced in Sparta, hence they had dispatched the hoplites.
See also point 4 about fining below. Late comers were disqualified! At the two hundred and eighteenth Festival that led to Heracleides winning without a contest!
1 Could be the first place at the pankratio, or his first victory. Pankratio itself was a highly regarded, full contact fight with elements of boxing and wrestling.
2 Main type of Greek heavy fighter, characterised by large shield, spear and short sword.
3 1mna = 100 drachmai
Pausanias Book 5 (Elis 1), Chapter 21, basically exclusively deals with fining athletes at the Olympics in detail. Since I never get around to finishing my own translation of this really long dedicated passage, I finally give in and provide the one by Jones et al. from Perseus.
Below I summarise: