As per my understanding, these are the possible reasons for missing data in Adobe Analytics UI/clickstream raw data when comparing with internal tools.
Any other reasons?
Add to the list
*the first two are a part of the implementation item, but do not have any relation to the code/SDK implementation.
Also take into account that sometimes the issue of data discrepancy is on the other end — internal tools.
Vista Rules specially like "IP Exclusion" "Moving hits from one report suite to other"
internal URL filters
Most common example listed here: Adobe Analytics Help | How to exclude data in Adobe Analytics