Using the aggregate plugin to zip the messages back together is problematic because ordering is not strictly maintained; the multiline messages will need to be grouped on the Filebeat side before being transmitted to Logstash.
If you are sending multiline events to Logstash, use the options described here to handle multiline events before sending the event data to Logstash. Trying to implement multiline event handling in Logstash (for example, by using the Logstash multiline codec) may result in the mixing of streams and corrupted data.
How is Filebeat configured? specifically, what are the values of the multiline.* fields?