I want to obtain all human homologous gene from a Ensembl.Gene.ID vector of all Mouse genes. The df i obtain is missing many entries. Also if I use gene names instead of the Ensemble ID I have the same Issues.

the getBM work fine 

What is wrong?

Thanks!

mart <- useMart(biomart = "ensembl", dataset = "mmusculus_gene_ensembl")
attributes = c("external_gene_name","entrezgene" ,"ensembl_gene_id", "description")
human = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
attributesL = c("entrezgene","hgnc_symbol", "ensembl_gene_id")
getLDS(attributes,  attributesL = attributesL, uniqueRows = T, filters = 'mgi_symbol', values=c("Cdkn2a"), mart = mart, martL = human)

[1] Associated.Gene.Name EntrezGene.ID        Ensembl.Gene.ID      Description          EntrezGene.ID.1    
[6] HGNC.symbol        
<0 rows> (or 0-length row.names)

getLDS(attributes,  attributesL = attributesL, uniqueRows = T, filters = 'ensembl_gene_id', values=c("ENSMUSG00000044303"), mart = mart, martL = human)
[1] Associated.Gene.Name EntrezGene.ID        Ensembl.Gene.ID      Description          EntrezGene.ID.1     
[6] HGNC.symbol         
<0 rows> (or 0-length row.names)

getBM(attributes, values = "ENSMUSG00000044303", filters = 'ensembl_gene_id', mart = mart)

  external_gene_name entrezgene    ensembl_gene_id                                                           description
1             Cdkn2a      12578 ENSMUSG00000044303 cyclin-dependent kinase inhibitor 2A [Source:MGI Symbol;Acc:MGI:104738]

I don't think this is a  problem with the biomaRt package, since I don't get any results if I use the web interface at www.ensembl.org/biomart either.  You can also get results for other gene IDs, so the code works.

getLDS(attributes, attributesL = attributesL, 
    uniqueRows = T, filters = 'mgi_symbol', values=c("OTOP3"), 
    mart = mart, martL = human)

  Associated.Gene.Name EntrezGene.ID    Ensembl.Gene.ID
1                Otop3         69602 ENSMUSG00000018862
                                      Description MGI.symbol
1 otopetrin 3 [Source:MGI Symbol;Acc:MGI:1916852]      Otop3
  EntrezGene.ID.1 HGNC.symbol Ensembl.Gene.ID.1
1          347741       OTOP3   ENSG00000182938

As you've already seen there are definitely Cdkn2a entries for both human and mouse, but they aren't classed as orthologs by Ensembl (you can see that listed here), and so you wouldn't expect to find them in the results here.