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The error happens when trying to intersect three layers, say A with B and then AB with C to get ABC. If same field names exist in all three layers the fields in the attribute table of ABC that correspond to C are messed up.

For example, I am trying to intersect the following three layers: Layer-A, Layer-B and Layer-C, of which the attribute tables have the fields displayed below. First, I am performing the intersection Layer-A + Layer-B (Vector -> Geoprocessing Tools -> Intersect) and then the Layer-A_Layer-B + Layer-C. The resulting Layer-A_Layer-B_Layer-C has some fields that came from the Layer-C messed up. I think this is caused because there is a field with the same name in all three layers (AREA). If I remove the field AREA from just Layer-C, then no problem.

Layer-A
-----------
Field 1: AREA
Field 2: HRU_CODE
Field 3: RNF_CF

Layer-B
-----------
Field 1: INI_LEVEL
Field 2: AREA
Field 3: GROUND_ID
Field 4: INI_LEV

Layer-C
-----------
Field 1: SUB_ID
Field 2: AREA
Field 3: NODE_ID