Problems working with GeoPackage, does not show all features

[hbecerraGIS]

What is the bug or the crash?

When working with GeoPackage two things happen:

It does not show all features on the map, neither in the attribute table nor in the feature count.

Shows all objects on the map and in the attribute table, but not the feature count.

With other formats such as shapefile and kml it does not happen

Steps to reproduce the issue

2022-12-18.12-40-59.mp4

2022-12-18.12-41-33.mp4

Versions

QGIS version
3.28.2-Firenze
QGIS code revision
b47e00b
Qt version
5.15.3
Python version
3.9.5
GDAL/OGR version
3.6.1
PROJ version
9.1.1
EPSG Registry database version
v10.076 (2022-08-31)
GEOS version
3.11.1-CAPI-1.17.1
SQLite version
3.39.4
PDAL version
2.4.3
PostgreSQL client version
unknown
SpatiaLite version
5.0.1
QWT version
6.1.6
QScintilla2 version
2.13.1
OS version
Windows 10 Version 2009

Active Python plugins
CalculateGeometry
0.6.8
EquirectangularViewer
1.4
GroupStats
2.2.6
kmltools
3.1.26
layer2kmz
1.5.3
loadthemall
3.3.0
mapswipetool_plugin
1.2
OpenTopography-DEM-Downloader
1.0
Qgis2threejs
2.7.1
qgis2web
3.16.0
quick_map_services
0.19.32
redLayer
2.2
rvt-qgis
0.9.4.1
slyr_community
4.0.6
wbt_for_qgis
1.0.5
db_manager
0.1.20
grassprovider
2.12.99
MetaSearch
0.3.6
processing
2.12.99
sagaprovider
2.12.99

Supported QGIS version

• I'm running a supported QGIS version according to the roadmap.

New profile

• I tried with a new QGIS profile

Additional context

I upgraded QGIS from 3.28.1 to 3.28.2 and the error remains

[nicogodet]

Was this gpkg created with 3.28.1 and potentially GDAL 3.6.0 ?
See #51188 ?

[nicogodet]

Could you share the data ?

[github-actions]

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[github-actions]

While we hate to see this happen, this issue has been automatically closed because it has not had any activity in the last 42 days despite being marked as feedback. If this issue should be reconsidered, please follow the guidelines in the previous comment and reopen this issue.
Or, if you have any further questions, there are also further support channels that can help you.

[gpointnerbbooe]

I had the same issue, presumably. The reason was that after editing the gpkg in QGIS (copying points from another layer multiple times and also deleting some points), the feature_count in gpkg_ogr_contents did not match the number of features in the main table anymore. I cannot reproduce what exactly caused the mismatch during editing, however.
The solution was to update the feature count again to match the number of features in the main table in sqlite:
UPDATE gpkg_ogr_contents set feature_count=(SELECT count(*) from table) where table_name='table';
Taken from here: https://gis.stackexchange.com/questions/429925/geopackage-sqlite-features-count-but-dont-exist-qgis
Hope this helps someone.