Please check the following sql query which will show the each user check in and check out details
select username,date,time as checkin, 0 as checkout, 0 as diff
into #temp from tablename as t
where t.indicator='Check-in'
update t set t.checkout=isnull((select top 1 a.time from tablename as a where a.username=t.username and a.date=t.date and a.indicator='Check-out' and a.time>t.checkin order by checkin desc),0)
from #temp as t
update t set t.diff=(checkout-checkin)
from #temp as t
select * from #temp