1.7.10/Forge 10.13.2.1272/BM 1.3.0a-1/HC 1.7.10f

For example, a 9x9 field of soybeans, when harvested manually, drops slightly below 2 stacks of soybeans.
That same field harvested with the Sigil drops half as much, less than one stack.

Pam's crops are set to be harvested by right-click, which causes them to drop one item less than if they would if set to be left-clicked like vanilla crops, and reset metadata to 0.
Perhaps Harvest Goddess Sigil erroneously does the same reduction? It definitely doesn't break and replant, as evidenced by my candleberries over grass from trampling still being there after sigil use.