The IRS has been very slow to notify people who miss their RMDs, so you are right, this is not at all unusual.
The IRS Regs seem to skip over the possibility of a multi year RMD omission and only clearly state that the RMD for the year of death (only for the year of death) is the responsibility of the beneficiary. If the beneficiary does not recognize the shortfall until a later year, they can take the missed RMD and request a waiver of the excess accumulation 50% penalty by filing Form 5329 and stating the "reasonable cause" for the omission. The IRS will likely waive any penalty.
But the bigger question here is what the IRS will do about all those previous years where they missed the tax revenue. They have not been aggressive about this, but am sure that if they wanted to they could levy a 50% excess accumulation penalty against the estate of the IRA owner. Have never heard of such a case, but it appears the IRS could do this.
Who is the IRA beneficiary?