Your post has been moved from the Update Announcement thread to a dedicated topic, as your query is not related to the Update.
I know nothing about the Flatpak External Data Checker at this time, except as it’s name seems to suggest. Was it installed as a part of the system, or did you install it from a foreign source (flatpak, the AUR, etc)?
From your description, it seems you might not be allowing enough time for Flatpak External Data Checker to finish before manually trying to update yourself. That being the case, it’s understandable, as only one package manager can run at any given time.
Because you have only given a vague description, and no actual error output, it’s difficult to know whether this is what happened; but it does seem likely.
Typically, run flatpak update after you’re certain that Flatpak External Data Checker (or any other package manager) has completed.
I’ve taken the liberty of linking to documentation for flatpak. Use these commands via the terminal as needed:
If you require further assistance, please provide the expected system information as described (below) and any other detail that might help others to assist you.
Regards.
Welcome to the Manjaro community
As a new or infrequent forum user, please take some time to familiarise yourself with Forum requirements, and the many ways to use the forum to your benefit.
To that end, links are provided (below) - Please use them.
Be prepared to provide outputs from various commands when asked. It’s equally important to provide as much actionable information as possible in your first post, rather than simply indicating there is a problem.
Waiting for someone to blindly ask questions is also counter-productive – typically, nobody has a 
at their disposal – Instead, please help others to ask informed questions, based on information you provide.
Update Announcements
The Update Announcements contain important information and a Known Issues and Solutions section that should generally be checked before posting a request for support.
System Information
While information from *-fetch type apps might be fine for someone wishing to buy your computer, for Support purposes it’s better to ask your system directly; 
Output of the inxi command (with appropriate parameters, and formatted according to forum guidelines) will generate information useful for those wishing to help:
inxi --filter --verbosity=8
or the short form (preferred):
inxi -zv8
- inxi man pages (Arch Manual)