did you figure it out? I have the same problem on Fedora Silverblue 38.
╰─$ flatpak info com.nextcloud.desktopclient.nextcloud
Nextcloud Desktop - Nextcloud desktop synchronization client
ID: com.nextcloud.desktopclient.nextcloud
Ref: app/com.nextcloud.desktopclient.nextcloud/x86_64/stable
Arch: x86_64
Branch: stable
Version: 3.9.1
License: GPL-2.0+
Origin: flathub
Collection: org.flathub.Stable
Installation: system
Installed: 183,7 MB
Runtime: org.kde.Platform/x86_64/5.15-22.08
Sdk: org.kde.Sdk/x86_64/5.15-22.08
Commit: ca61127ad56eec7061cb31dd500d3feb60263792d8d095fa8ee8090866bb8d3a
Parent: 2be08afea65b96f9a6a3801a87d04b971cbf869cf32647f7e95822b12c2ae0c6
Subject: Update desktop.git to 3.9.1 (67864904)
Date: 2023-07-25 22:01:39 +0000
I don’t know if this is just related to tray, which doesn’t exist in gnome3, or to the problem at hand:
2023-07-31 22:02:11:970 [ warning default qrc:/qml/src/gui/tray/AutoSizingMenu.qml:11 ]: qrc:/qml/src/gui/tray/AutoSizingMenu.qml:11: TypeError: Cannot read property 'implicitWidth' of undefined
2023-07-31 22:02:14:742 [ warning default qrc:/qml/src/gui/tray/AutoSizingMenu.qml:11 ]: qrc:/qml/src/gui/tray/AutoSizingMenu.qml:11: TypeError: Cannot read property 'implicitWidth' of undefined
2023-07-31 22:02:17:929 [ info nextcloud.gui.application /run/build/nextcloud-client/src/gui/application.cpp:981 ]: Trying tray icon, tray available: false