I get this exception with the file amyuni2_05d__pdf1_3_acro4x.pdf (it was once part of the project, now no more, but it can still be found on the web):
java.io.IOException: Object (48:0) at offset 161333 does not end with 'endobj'.
This is true, the "endobject" is indeed missing in that file. However the content of endObjectKey is 49 0 obj, i.e. the start of a new object.