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I checked all of the 1041s I have prepared. The error does not occur when there is a total capital loss (which makes sense because a loss cannot be allocated to a beneficiary), or when there is no capital gain allocated to the beneficiary. It only occurs when there is an amount of capital gain less than the total capital gain allocated to the beneficiary, in which case the program transfers the total capital gain rather than the amount allocated.
The default rule for trusts is that capital gain is not allocated to beneficiaries, but there are three exceptions in the Regs. The program allocated over a half million in capital gain to a beneficiary on line 3 even though about $100k was specified on Sch D, and the beneficiary only received about $100k in distributions -- impossible!