Error while removing gaps with v.clean in QGIS

I have a polygon layer (Geopackage with 378 features in EPSG:3857) with many very small gaps between them (topology checker lists more than 5000). The gaps are in a range of several hundred meters to fractions of millimeters in map units (meters). Using QGIS 3.16, I tried Grass v.clean. However, it is not able to repair the geometries. No output is generated.

Error messages in the protocol mention:

ERROR 1: osgeo::proj::io::WKTParser::Private::buildEllipsoid: non
double value

WARNING: Unable to determine input map’s vector feature type(s).

ERROR: Unable to create OGR spatial reference

I tried also QGIS native repair geometries as well as fill gaps algorithm – the resulting output has the same gaps.

What else could I try to remove these gaps?