This is related to #3846 / #3849.

Given the following FEA (from NotoSansMalayalam.glyphs),

feature blwf {
    # GSUB feature: Below-base Forms
    # Lookups: 2
    script mlym;
    # Malayalam
    sub lamlym viramamlym by lasubscriptmlym;
    sub lasubscriptmlym by viramamlym lamlym;
    language MAL;
    # Malayalam
} blwf;

feaLib generates two lookups, but fails to add the second lookup to the feature.

I presume this is because the lookup is added to the feature when the rule is encountered, and at that point both rules share a single lookup; the lookups are split afterwards.

cc @khaledhosny, not sure if there's a reasonably simple fix for this?