When ingesting an bitstream to an Item (i.e. adding a file to the media resource), BinaryContentIngester creates a new ORIGINAL bundle even if one is already available. Also, it does not set the MIME-type for the bitstream.
The problem is in BinaryContentIngester, line 138:
Bundle original = null;
original is assigned but never used because at lines 148:
Bitstream bs = item.createSingleBitstream(deposit.getInputStream());
which creates a new bundle disregarding the original bundle.
This code should solve the problem, and also add the bitstream format field:
Bitstream bs = original.createBitstream(deposit.getInputStream());
BitstreamFormat format = this.getFormat(context,deposit.getFilename());