Three points missing in NMDS graph

Question

see image of some of my data x12 locations x26 macroinvertebrates

Hello, this is my first time producing an NMDS graph. I am missing three sites from the final plot (Creek B1,B2,B3).
I looked at the scores to see there was four with the exact same scores- this seems suspicious to me ? This data was collected by students though and with not much rigour so may be a combination of sample error and my code.

Here is my code:

library("vegan")
library(readxl)
rivers_catchement <- read_excel("rivers_catchement.xlsx", 
   sheet = "Sheet1")

### *Step 1. subset data which contains values:*

data_1<-rivers_catchement[,2:26]

### *Step 2. subset data contains locations:*
data_2<-rivers_catchement[1]

set.seed(3)
library("vegan")
NMDS<-metaMDS(data_1, distance= "bray")

NMDS$stress

2 0.07057647 (stress output)

set.seed(3)
library("vegan")
library("ggplot2")
scores<-scores(NMDS, display="site")

scores <- cbind(as.data.frame(scores), Habitat = data_2$Habitat)
centroids <- aggregate(cbind(NMDS1, NMDS2) ~ Habitat, data = scores, FUN = mean)
seg <- merge(scores, setNames(centroids, c('Habitat','oNMDS1','oNMDS2')),
             by = 'Habitat', sort = FALSE)

ggplot(scores, aes(x = NMDS1, y = NMDS2, colour = Habitat))+
scale_color_manual(values=c("seagreen4", "olivedrab", "palegreen3",
                              "darkcyan", "cornflowerblue", "deepskyblue3",
                              "coral1", "sienna3","brown2", "indianred3",
                              "maroon", "palevioletred"))+
  geom_segment(data = seg,
               mapping = aes(xend = oNMDS1, yend = oNMDS2)) + 
  geom_point(data = centroids, size = 4) +                    
  geom_point() + 
 
   geom_text(label= data_2$Habitat, 
    nudge_x = 0.10, nudge_y = 0.05, 
    check_overlap = T)+
  ggtitle("NMDS To Represent Macroinvertebrate Assembleges 
          Across Sites Within Leaf Litter")+
  theme(plot.title = element_text(hjust = 0.5), 
        text = element_text(family = "Times New Roman"))

If i set check_overlap = F I believe all the points are there but it is difficult to read. see here

Any tips on how to improve would help Thanks in advance for the help!