Ok I found the problem, your file clements-sample.csv has a "latin1" encoding and includes a rare non-breaking space character \xa0 if I remove this character, it works as expected.
I suppose you don't get to see it, because, since you speak spanish, very likely your OS is using the same encoding, so for you, it just looks like a regular empty space with nothing special about it.
library(dplyr)
species_sample<-read.csv("clements-sample.csv", header = FALSE, skip = 1)
species_sample_mtx<-as.matrix(species_sample)
species_sample_vct<-as.vector(species_sample_mtx)
species_sample_vct <- stringr::str_replace(species_sample_vct, "\xa0", " ")
BDGP<-read.csv("BDGP1.csv", header = TRUE)
BDGP_select <- select(BDGP, Nro, Especie)
BDGP_sample <- BDGP_select[c(180:190),]
BDGP_sample %>%
mutate(Especie = as.character(Especie)) %>%
filter(Especie %in% species_sample_vct)
#> Nro Especie
#> 1 639 Saltator coerulescens
#> 2 700 Leistes superciliaris