@hclc, which couchbase version are you using? If you are on 4.5.0, please switch to Circular Write Mode. (change compaction mode from UI “Settings” → “Auto Compaction” → “Index Fragmentation” → “Circular Write Mode”).
In general, Indexer save 5 snapshots of data(at different points in time) for recovery. This can lead to more disk space usage than data size. Also the storage itself has write amplification due to MVCC architecture. When the compaction is in progress, data on the disk gets duplicated when the new compacted file gets created.
The write amplification can be prevented to a large extent by using Circular Write Mode in 4.5.0. More details here:
http://developer.couchbase.com/documentation/server/4.5/indexes/gsi-for-n1ql.html