We found this issue because a search for biblionumber=XX would not bring up the right record in the database, but the record with the matching biblioitemnumber. 

999$c = biblionumber
999$d = biblioitemnumber

http://bernina.bsz-bw.de/gitweb/?p=koha.git;a=blob;f=etc/zebradb/marc_defs/marc21/biblios/biblio-koha-indexdefs.xml;h=06b52f71709cbe40eca5506c7c04106a81682424;hb=0c349b45f5bb6145af3c5db966e28946b1cc0e11

biblio-koha-indexdefs.xml

<index_subfields tag="999" subfields="c">
 <target_index>Local-Number:n</target_index>
 <target_index>Local-Number:w</target_index>
 <target_index>Local-Number:s</target_index>
</index_subfields>

<index_subfields tag="999" subfields="d">
 <target_index>biblioitemnumber:n</target_index>
 <target_index>biblioitemnumber:w</target_index>
 <target_index>biblioitemnumber:s</target_index>
</index_subfields>

bernina.bsz-bw.de/gitweb/?p=koha.git;a=blob;f=etc/zebradb/biblios/etc/bib1.att;h=24164431ce536750849a0fa8b02c5806bf8e297e;hb=0c349b45f5bb6145af3c5db966e28946b1cc0e11

bib1.att says:
att 12    Local-number
att 9002    biblioitemnumber

But: http://git.koha-community.org/gitweb/?p=koha.git;a=blob;f=etc/zebradb/ccl.properties;h=5c003d301d952d984616f79fe8f796f75843927c;hb=df611b17d12b63bb2f14909969ff8e8f67a332d0

ccl.properties has the error:

Local-number 1=12
sn Local-number

biblionumber 1=9002

Should be:

Local-number 1=12
sn Local-number
biblionumber Local-number

biblioitemnumber 1=9002