I got worried about the same error message, but turns out it seems to be an internal error while trying to find an existing compaction file that should probably not have been logged by CouchDB. If you change your log level to "debug", you'll notice that it completes the compaction despite the error that was shown:
[info] [<0.319.0>] Starting compaction for db "core-configuration"
[debug] [<0.896.0>] Compaction process spawned for db "core-configuration"
[info] [<0.130.0>] 192.168.1.20 - - POST /core-configuration/_compact 202
[error] [<0.896.0>] Could not open file /var/data/couchdb/core-configuration.couch.compact: no such file or directory
[debug] [<0.88.0>] New task status for <0.896.0>: [{changes_done,3981},
{database,
<<"core-configuration">>},
{progress,49},
{started_on,1368262489},
{total_changes,8082},
{type,database_compaction},
{updated_on,1368262490}]
[debug] [<0.88.0>] New task status for <0.896.0>: [{changes_done,7959},
{database,
<<"core-configuration">>},
{progress,98},
{started_on,1368262489},
{total_changes,8082},
{type,database_compaction},
{updated_on,1368262492}]
[debug] [<0.319.0>] CouchDB swapping files /var/data/couchdb/core-configuration.couch and /var/data/couchdb/core-configuration.couch.compact.
[info] [<0.319.0>] Compaction for db "core-configuration" completed.