Actually, this happens also to other use cases of getSeq (the code below is taken from GenomicFeatures extractTranscriptSeqs help page):

library(GenomicFeatures)
library(BSgenome.Hsapiens.UCSC.hg19)
genome <- BSgenome.Hsapiens.UCSC.hg19

## Load a TxDb object:
txdb_file <- system.file("extdata", "hg19_knownGene_sample.sqlite",
                         package="GenomicFeatures")
txdb <- loadDb(txdb_file)

## Check that 'txdb' is based on the hg19 assembly:
txdb

## Extract the exon ranges grouped by transcript from 'txdb':
transcripts <- exonsBy(txdb, by="tx", use.names=TRUE)

## Extract the transcript sequences from the genome:
tx_seqs <- extractTranscriptSeqs(genome, transcripts)
tx_seqs

Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) :
  subscript contains NAs or out-of-bounds indices

Eventually this is caused by some updated package. I remember I did a package update today, but I can't remember which packages got updated (IRanges?).

Did you also update your packages recently?

cheers, jo

My session info:

> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-apple-darwin15.0.0/x86_64 (64-bit)
Running under: OS X 10.11.2 (El Capitan)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets
[8] methods   base     

other attached packages:
 [1] GenomicFeatures_1.22.4            AnnotationDbi_1.32.0             
 [3] Biobase_2.30.0                    BSgenome.Hsapiens.UCSC.hg19_1.4.0
 [5] BSgenome_1.38.0                   rtracklayer_1.30.1               
 [7] Biostrings_2.38.1                 XVector_0.10.0                   
 [9] GenomicRanges_1.22.1              GenomeInfoDb_1.6.1               
[11] IRanges_2.4.2                     S4Vectors_0.8.3                  
[13] BiocGenerics_0.16.1              

loaded via a namespace (and not attached):
 [1] zlibbioc_1.16.0            GenomicAlignments_1.6.1   
 [3] BiocParallel_1.4.0         tools_3.2.2               
 [5] SummarizedExperiment_1.0.1 DBI_0.3.1                 
 [7] lambda.r_1.1.7             futile.logger_1.4.1       
 [9] futile.options_1.0.0       bitops_1.0-6              
[11] biomaRt_2.26.0             RCurl_1.95-4.7            
[13] RSQLite_1.0.0              Rsamtools_1.22.0          
[15] XML_3.98-1.3