Is this internal logic intentional? makes no sense to me.

# Goal: insert b or bmeta in index 1 of a
# Will fail if metadata is of type GRangesList and length > 1.

library(GenomicRanges)
b <- bmeta <- GRanges("1", IRanges(c(1, 3), width = 1), "+")
bmeta$ref <- GRangesList(GRanges("1", IRanges(c(1, 3), width = 1), "+"))

# This will not crash
a <- GRangesList(GRanges())
a[[1]] <- b
# This not will crash
a <- GRangesList(GRanges())
a[[1]] <- bmeta[1]
a[[1]] <- bmeta
# This will crash
a <- GRangesList(GRanges())
a[[1]] <- bmeta

sessionInfo( )
R version 4.1.0 (2021-05-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.3 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=nb_NO.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=nb_NO.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=nb_NO.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=nb_NO.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] ORFquant_1.02.0             rmarkdown_2.11              reshape2_1.4.4             
 [4] multitaper_1.0-15           knitr_1.36                  gridExtra_2.3              
 [7] ggplot2_3.3.5               GenomicFiles_1.28.0         BiocParallel_1.28.0        
[10] doMC_1.3.7                  iterators_1.0.13            foreach_1.5.1              
[13] devtools_2.4.2              usethis_2.0.1               cowplot_1.1.1              
[16] BSgenome_1.61.0             rtracklayer_1.54.0          GenomicFeatures_1.46.1     
[19] AnnotationDbi_1.56.0        uORFomePipe_0.2.0           data.table_1.14.2          
[22] DBI_1.1.1                   RiboCrypt_1.1.1             ORFik_1.15.6               
[25] GenomicAlignments_1.30.0    Rsamtools_2.10.0            Biostrings_2.62.0          
[28] XVector_0.33.0              SummarizedExperiment_1.23.5 Biobase_2.53.0             
[31] MatrixGenerics_1.5.4        matrixStats_0.61.0          GenomicRanges_1.46.0       
[34] GenomeInfoDb_1.30.0         IRanges_2.28.0              S4Vectors_0.32.2           
[37] BiocGenerics_0.40.0        

loaded via a namespace (and not attached):
  [1] readxl_1.3.1             backports_1.2.1          BiocFileCache_2.1.1     
  [4] plyr_1.8.6               lazyeval_0.2.2           splines_4.1.0           
  [7] digest_0.6.28            h2o_3.32.1.3             htmltools_0.5.2         
 [10] fansi_0.5.0              magrittr_2.0.1           memoise_2.0.0           
 [13] remotes_2.4.1            openxlsx_4.2.4           annotate_1.71.0         
 [16] R.utils_2.11.0           prettyunits_1.1.1        colorspace_2.0-2        
 [19] blob_1.2.2               rappdirs_0.3.3           xfun_0.26               
 [22] haven_2.4.3              dplyr_1.0.7              callr_3.7.0             
 [25] crayon_1.4.1             RCurl_1.98-1.5           jsonlite_1.7.2          
 [28] genefilter_1.75.1        VariantAnnotation_1.38.0 survival_3.2-13         
 [31] glue_1.4.2               gtable_0.3.0             zlibbioc_1.39.0         
 [34] DelayedArray_0.19.4      pkgbuild_1.2.0           car_3.0-11              
 [37] biomartr_0.9.2           abind_1.4-5              scales_1.1.1            
 [40] futile.options_1.0.1     GGally_2.1.2             rstatix_0.7.0           
 [43] Rcpp_1.0.7               viridisLite_0.4.0        xtable_1.8-4            
 [46] progress_1.2.2           foreign_0.8-81           bit_4.0.4               
 [49] htmlwidgets_1.5.3        httr_1.4.2               RColorBrewer_1.1-2      
 [52] ellipsis_0.3.2           pkgconfig_2.0.3          reshape_0.8.8           
 [55] XML_3.99-0.8             R.methodsS3_1.8.1        dbplyr_2.1.1            
 [58] locfit_1.5-9.4           utf8_1.2.2               tidyselect_1.1.1        
 [61] rlang_0.4.11             munsell_0.5.0            cellranger_1.1.0        
 [64] tools_4.1.0              cachem_1.0.6             cli_3.0.1               
 [67] generics_0.1.0           RSQLite_2.2.8            broom_0.7.9             
 [70] evaluate_0.14            stringr_1.4.0            fastmap_1.1.0           
 [73] yaml_2.2.1               processx_3.5.2           fs_1.5.0                
 [76] bit64_4.0.5              zip_2.2.0                purrr_0.3.4             
 [79] lemon_0.4.5              KEGGREST_1.33.0          formatR_1.11            
 [82] R.oo_1.24.0              xml2_1.3.2               biomaRt_2.49.4          
 [85] compiler_4.1.0           rstudioapi_0.13          plotly_4.10.0           
 [88] filelock_1.0.2           curl_4.3.2               png_0.1-7               
 [91] testthat_3.1.0           ggsignif_0.6.3           tibble_3.1.5            
 [94] geneplotter_1.71.0       stringi_1.7.5            ps_1.6.0                
 [97] futile.logger_1.4.3      desc_1.4.0               forcats_0.5.1           
[100] lattice_0.20-45          Matrix_1.3-4             vctrs_0.3.8             
[103] pillar_1.6.3             lifecycle_1.0.1          BiocManager_1.30.16     
[106] bitops_1.0-7             R6_2.5.1                 BiocIO_1.4.0            
[109] rio_0.5.27               codetools_0.2-18         sessioninfo_1.1.1       
[112] lambda.r_1.2.4           pkgload_1.2.3            assertthat_0.2.1        
[115] rprojroot_2.0.2          DESeq2_1.33.5            rjson_0.2.20            
[118] withr_2.4.2              GenomeInfoDbData_1.2.7   hms_1.1.0               
[121] fst_0.9.4                VennDiagram_1.6.20       tidyr_1.1.4             
[124] carData_3.0-4            ggpubr_0.4.0             restfulr_0.0.13

It's obviously a bug and I don't see any crash. Fixed in S4Vectors 0.32.3 (release) and 0.33.4 (devel).

Also a better place to report bugs is to open an issue on GitHub.

Cheers,

H.