Ginormous coincidences?

Supposing they don’t wish to admit the criticisms are largely correct (whether taking responsibility or blaming others), broadly speaking the accused has the following options:

1. Full Rebuttal: Carefully show that all criticisms are either based on explicit errors, or that there are innocent explanations for all suspicious-seeming facts.
2. Partial Rebuttal: Find specific points on which the criticism oversteps or involves errors, rebut those, and treat this as undermining the aggregate accusations.
3. Muddy the Waters: Deny the accusations, and attempt to obfuscate and muddy the waters. Typically this may involve raising a lot of difficult-to-litigate technical detail - relatively few people (even amongst academics) will expend the effort required to determine if one party is definitively right once a dispute gets bogged down in interminable detail. Similar to criminal trials, creating reasonable doubt is generally sufficient to save someone’s reputation.

A truly innocent party will naturally prefer Option 1 to Option 2 and so forth. A party that is truly guilty (whether of fraud, or merely of screwing up) doesn’t have a tenable path to achieving Option 1, and will prefer Option 2 to Option 3 if both are feasible. Someone who attempts to muddy the waters is implicitly admitting that this is their best option, suggesting that the criticisms probably are valid. But probably can leave residual doubt, and furthermore, there’s no magic bullet to tell Options 1-3 apart. For example, sometimes the correct rebuttal requires large amounts of technical detail.