gtk_tree_column_set_visible code does:

priv->visible = visible;
_gtk_tree_view_accessible_toggle_visibility (GTK_TREE_VIEW (priv->tree_view), tree_column);


_gtk_tree_view_accessible_toggle_visibility then uses:
id = get_column_number (treeview, column);

get_column_number iterates over the treeview columns and skip the non-visible ones. If it could not find the column, it outputs a runtime warning through 
g_return_val_if_fail (i < gtk_tree_view_get_n_columns (treeview), 0);

When hiding a column, the column will be marked as non-visible before get_column_number is called, so this function will skip the column as it's non visible, and will then outputs a runtime warning. The a11y code will then mark the column 0 as visible/non-visible instead of working with the right column.