Media Library nonfunctional because of nonexisting images

Hi,

I’m running multisite server, after upgrading to WordPress 4.6.1 Media Library on one of the sites only works in list view and shows number of non existing images. I have no way of removing them and they break Media Library. One of the issues is not showing any new additions to Library, even though they are in the upload folder.

I’m getting following errors when enabled debug mode:
Notice: Trying to get property of non-object in ../wordpress/wp-includes/post.php on line 5551
Notice: Trying to get property of non-object in ../wordpress/wp-admin/includes/class-wp-media-list-table.php on line 615

Notice: Trying to get property of non-object in ../wordpress/wp-admin/includes/class-wp-media-list-table.php on line 349
Notice: Trying to get property of non-object in ../wordpress/wp-admin/includes/class-wp-media-list-table.php on line 366
Notice: Trying to get property of non-object in ../wordpress/wp-admin/includes/class-wp-media-list-table.php on line 369
Notice: Trying to get property of non-object in ../wordpress/wp-includes/media.php on line 856
Notice: Trying to get property of non-object in ../wordpress/wp-includes/media.php on line 858
Notice: Trying to get property of non-object in ../wordpress/wp-admin/includes/class-wp-media-list-table.php on line 372
Notice: Trying to get property of non-object in ../wordpress/wp-admin/includes/template.php on line 1765
Notice: Trying to get property of non-object in ../wordpress/wp-admin/includes/template.php on line 1769
Notice: Trying to get property of non-object in ../wordpress/wp-admin/includes/class-wp-media-list-table.php on line 397
Notice: Trying to get property of non-object in ../wordpress/wp-admin/includes/class-wp-media-list-table.php on line 699
Notice: Trying to get property of non-object in ../wordpress/wp-admin/includes/class-wp-media-list-table.php on line 708
Notice: Trying to get property of non-object in ../wordpress/wp-admin/includes/class-wp-media-list-table.php on line 741

Notice: Trying to get property of non-object in ../wordpress/wp-admin/includes/class-wp-media-list-table.php on line 468
Notice: Trying to get property of non-object in ../wordpress/wp-admin/includes/class-wp-media-list-table.php on line 470

Notice: Trying to get property of non-object in ../wordpress/wp-admin/includes/class-wp-media-list-table.php on line 531
Notice: Trying to get property of non-object in ../wordpress/wp-admin/includes/class-wp-media-list-table.php on line 534
Notice: Trying to get property of non-object in ../wordpress/wp-admin/includes/class-wp-media-list-table.php on line 537

Notice: Trying to get property of non-object in ../wordpress/wp-admin/includes/class-wp-media-list-table.php on line 440
Notice: Trying to get property of non-object in ../wordpress/wp-admin/includes/class-wp-media-list-table.php on line 443

I’m guessing the problem would be resolved if I could get rid of those non existing images but I don’t know how, any suggestion would be appreciated.