When the value of a Number field is shown in a post list column cell, the plugin will apply its own number formatting (i.e. thousands separators) to the value.
This appears to be applied after any presentation defined in acf/format_value filters. Thus, for Number fields where thousands separators are not appropriate (e.g. year, numeric ID, serial number, etc), there doesn't appear to be any way to turn these off, or otherwise override or define the presentation on a field-by-field basis.