The reason they are being shown as checked out with the report sent is because their report was created late in the day yesterday. The sent report will be from the day before.
HiMama works on a 16 hour system; once a report is created, it alerts the system that a day has begun and 16 hours from then the day will refresh. This is done to accommodate for different time zones and overnight centers. Since they were checked in fewer than 16 hours ago, the child is still registered as "Checked Out".
Navigate to the relevant class for the child, and select the "Classroom Actions" button.
From the dropdown menu, select "Enrollment".
Select the "Actions" button, and "Check In" for the relevant child.