Description of problem:
Looks like the privileged system helper for flatpak isn't allowed to run successfully.

Running "flatpak update" as a normal user reports "Looking for updates… Nothing to do." as usual, but the process then doesn't terminate.
SELinux is preventing (m-helper) from 'execute' accesses on the file flatpak-system-helper.

*****  Plugin catchall (100. confidence) suggests   **************************

If you believe that (m-helper) should be allowed execute access on the flatpak-system-helper file by default.
Then you should report this as a bug.
You can generate a local policy module to allow this access.
Do
allow this access for now by executing:
# ausearch -c '(m-helper)' --raw | audit2allow -M my-mhelper
# semodule -X 300 -i my-mhelper.pp

Additional Information:
Source Context                system_u:system_r:init_t:s0
Target Context                system_u:object_r:unlabeled_t:s0
Target Objects                flatpak-system-helper [ file ]
Source                        (m-helper)
Source Path                   (m-helper)
Port                          <Unknown>
Host                          (removed)
Source RPM Packages           
Target RPM Packages           
Policy RPM                    selinux-policy-3.14.4-43.fc31.noarch
Selinux Enabled               True
Policy Type                   targeted
Enforcing Mode                Enforcing
Host Name                     (removed)
Platform                      Linux (removed) 5.3.15-300.fc31.x86_64 #1 SMP Thu
                              Dec 5 15:04:01 UTC 2019 x86_64 x86_64
Alert Count                   1
First Seen                    2019-12-08 12:11:09 CET
Last Seen                     2019-12-08 12:11:09 CET
Local ID                      e3d31223-df50-47be-a9cd-e37ca0c83cc5

Raw Audit Messages
type=AVC msg=audit(1575803469.840:287): avc:  denied  { execute } for  pid=3523 comm="(m-helper)" name="flatpak-system-helper" dev="nvme0n1p3" ino=100154800 scontext=system_u:system_r:init_t:s0 tcontext=system_u:object_r:unlabeled_t:s0 tclass=file permissive=0 trawcon="system_u:object_r:flatpak_helper_exec_t:s0"


Hash: (m-helper),init_t,unlabeled_t,file,execute

Version-Release number of selected component:
selinux-policy-3.14.4-43.fc31.noarch

Additional info:
component:      selinux-policy
reporter:       libreport-2.11.3
hashmarkername: setroubleshoot
kernel:         5.3.15-300.fc31.x86_64
type:           libreport

Potential duplicate: bug 1764538