In EMS server log, sometimes it is shown that messages are being expired. 

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2018-05-09 08:21:02.756 Expired 2 messages.
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Run tibemsminitor under <ems_home>/bin covering the time "Expired xxx messages" is logged by EMS.

For queue:

tibemsmonitor -m 'Q.p.>' -user admin -password <password>

For topic:

tibemsmonitor -m 'T.p.>' -user admin -password <password>

Sample output from tibemsmonitor:

=====
2018-01-19 11:10:02.565 [EMS-SERVER] $sys.monitor.Q.p.queue.exp
    event_action      = string:  'premature_exit'
    event_class       = string:  'message'
    event_reason      = string:  'expired'
    JMSXDeliveryCount = int:     1
...
    target_dest_name  = string:  'queue.exp'
    target_dest_type  = string:  'queue'
    BytesMessage={Header={ JMSDestination={QUEUE:'queue.exp'} JMSDeliveryMode={NON_P
SCorrelationID={c123} JMSTimestamp={Fri Jan 19 11:09:54 2018} JMSDeliveryTime={Fri J
{int:1}} Body={byte[]:0 bytes}
=====
Please refer to EMS User's Guide: Chapter 19 Monitoring Server Activity : Monitoring Server Events.

As expiration can be set either in message itself or destination, it may not be straightforward to find what messages are being expired and the destination they are sent to.

EMS User's Guide: Chapter 19 Monitoring Server Activity : Monitoring Server Events.