We observed this issue also, but i guess it's not a parse problem, since the segments regenerated in the following task and finally published successful.
A little different is that in my case the exception is reported when serialize the metadata:
2019-01-29T13:30:48,059 INFO [access_log-incremental-persist] io.druid.segment.realtime.appenderator.AppenderatorImpl - Committing metadata[AppenderatorDriverMetadata{segments={****}].
2019-01-29T13:30:48,060 INFO [task-runner-0-priority-0] io.druid.segment.realtime.appenderator.StreamAppenderatorDriver - Persisted pending data in 48ms.
2019-01-29T13:30:48,064 INFO [task-runner-0-priority-0] io.druid.segment.realtime.appenderator.AppenderatorImpl - Shutting down immediately...
2019-01-29T13:30:48,065 INFO [task-runner-0-priority-0] io.druid.server.coordination.BatchDataSegmentAnnouncer - Unannouncing segment[***] at path[/druid/segments/emr-worker-4.cluster-72321:8101/emr-worker-4.cluster-72321:8101_indexer-executor__default_tier_2019-01-29T12:50:13.319Z_51df8fd2617a48868262f617e05efb170]
2019-01-29T13:30:48,066 INFO [task-runner-0-priority-0] io.druid.server.coordination.BatchDataSegmentAnnouncer - Unannouncing segment[***] at path[/druid/segments/emr-worker-4.cluster-72321:8101/emr-worker-4.cluster-72321:8101_indexer-executor__default_tier_2019-01-29T12:50:13.319Z_51df8fd2617a48868262f617e05efb170]
2019-01-29T13:30:48,067 INFO [task-runner-0-priority-0] io.druid.server.coordination.BatchDataSegmentAnnouncer - Unannouncing segment[***] at path[/druid/segments/emr-worker-4.cluster-72321:8101/emr-worker-4.cluster-72321:8101_indexer-executor__default_tier_2019-01-29T12:50:13.319Z_51df8fd2617a48868262f617e05efb170]
2019-01-29T13:30:48,067 INFO [task-runner-0-priority-0] io.druid.curator.announcement.Announcer - unannouncing [/druid/segments/emr-worker-4.cluster-72321:8101/emr-worker-4.cluster-72321:8101_indexer-executor__default_tier_2019-01-29T12:50:13.319Z_51df8fd2617a48868262f617e05efb170]
2019-01-29T13:30:48,088 INFO [task-runner-0-priority-0] io.druid.segment.realtime.firehose.ServiceAnnouncingChatHandlerProvider - Unregistering chat handler[***]
2019-01-29T13:30:48,088 INFO [task-runner-0-priority-0] io.druid.curator.discovery.CuratorDruidNodeAnnouncer - Unannouncing [DiscoveryDruidNode{druidNode=DruidNode{serviceName='druid/middleManager', host='emr-worker-4.cluster-72321', port=-1, plaintextPort=8101, enablePlaintextPort=true, tlsPort=-1, enableTlsPort=false}, nodeType='peon', services={dataNodeService=DataNodeService{tier='_default_tier', maxSize=0, type=indexer-executor, priority=0}, lookupNodeService=LookupNodeService{lookupTier='__default'}}}].
2019-01-29T13:30:48,088 INFO [task-runner-0-priority-0] io.druid.curator.announcement.Announcer - unannouncing [/druid/internal-discovery/peon/emr-worker-4.cluster-72321:8101]
2019-01-29T13:30:48,092 INFO [task-runner-0-priority-0] io.druid.curator.discovery.CuratorDruidNodeAnnouncer - Unannounced [DiscoveryDruidNode{druidNode=DruidNode{serviceName='druid/middleManager', host='emr-worker-4.cluster-72321', port=-1, plaintextPort=8101, enablePlaintextPort=true, tlsPort=-1, enableTlsPort=false}, nodeType='peon', services={dataNodeService=DataNodeService{tier='_default_tier', maxSize=0, type=indexer-executor, priority=0}, lookupNodeService=LookupNodeService{lookupTier='__default'}}}].
2019-01-29T13:30:48,092 INFO [task-runner-0-priority-0] io.druid.server.coordination.CuratorDataSegmentServerAnnouncer - Unannouncing self[DruidServerMetadata{name='emr-worker-4.cluster-72321:8101', hostAndPort='emr-worker-4.cluster-72321:8101', hostAndTlsPort='null', maxSize=0, tier='_default_tier', type=indexer-executor, priority=0}] at [/druid/announcements/emr-worker-4.cluster-72321:8101]
2019-01-29T13:30:48,092 INFO [task-runner-0-priority-0] io.druid.curator.announcement.Announcer - unannouncing [/druid/announcements/emr-worker-4.cluster-72321:8101]
2019-01-29T13:30:48,095 ERROR [task-runner-0-priority-0] io.druid.indexing.overlord.ThreadPoolTaskRunner - Exception while running task[KafkaIndexTask{id=index_kafka_access_log_5855cca6d6ce7d7_ojahebcn, type=index_kafka, dataSource=access_log}]
java.lang.IllegalArgumentException: fromIndex(0) > toIndex(-1)
at java.util.ArrayList.subListRangeCheck(ArrayList.java:1012) ~[?:1.8.0_151]
at java.util.ArrayList.subList(ArrayList.java:1002) ~[?:1.8.0_151]
at io.druid.segment.realtime.appenderator.AppenderatorImpl.persistAll(AppenderatorImpl.java:408) ~[druid-server-0.12.1.jar:0.12.1]
at io.druid.segment.realtime.appenderator.AppenderatorImpl.push(AppenderatorImpl.java:519) ~[druid-server-0.12.1.jar:0.12.1]
at io.druid.segment.realtime.appenderator.BaseAppenderatorDriver.pushInBackground(BaseAppenderatorDriver.java:351) ~[druid-server-0.12.1.jar:0.12.1]
at io.druid.segment.realtime.appenderator.StreamAppenderatorDriver.publish(StreamAppenderatorDriver.java:268) ~[druid-server-0.12.1.jar:0.12.1]