diff --git a/src/mito2/src/compaction.rs b/src/mito2/src/compaction.rs
index dbd1739716..7d4302cb74 100644
--- a/src/mito2/src/compaction.rs
+++ b/src/mito2/src/compaction.rs
@@ -1006,6 +1006,8 @@ impl CompactionSstReaderBuilder<'_> {
     /// for compaction. The schema of the [FlatSource] is unified.
     async fn build_flat_sst_reader(self) -> Result<FlatSource> {
         let scan_input = self.build_scan_input().await?.with_compaction(true);
+        // Compaction reads/writes flat SST batches (with internal columns), so this must use
+        // the flat input schema instead of the logical output schema.
         let schema = scan_input.mapper.input_arrow_schema(scan_input.compaction);
 
         let stream = SeqScan::new(scan_input)