I am trying to check beta diversity with Adonis and comparing the result with a plot in ggplot2. Adonis gives me a significant difference between 2 groups but the plot shows no separation of profiles. I suspect and error in my code for the plot. Would anyone have an idea?

This is my code for the plot:

f <- read_xlsx("dataset.xlsx")
f1 <- f[,-1:-2]    # remove column names

dist <- vegdist(f1, method = "bray")

pcoa <- cmdscale(dist, k=2, eig=TRUE, add=TRUE)   # eig needed for percentage explained, 'add' makes all eig positive
positions <- pcoa$points       #pcoa is a list after line 14, has to be changed to be used in ggplot
colnames(positions) <- c("PCoA1", "PCoA2")

pcoa$eig

percent_explained1 <- 100 * pcoa$eig / sum(pcoa$eig)    #data for axes
percent_explained1[1:2] 

d_mat <- as.data.frame(positions)
fig_f <- f[,1:2]
d_set <- cbind(d_mat, fig_f) 

centroid <- d_set%>%
  group_by(sample_name_lims) %>%
  summarize(PCoA1 = mean(PCoA1),
            PCoA2 = mean(PCoA2))

ggplot(d_set, aes(x=PCoA1, y=PCoA2, color=sample_name_lims)) +     
  geom_point() +
  geom_point(data=centroid,
             mapping=aes(x=PCoA1, y=PCoA2, color=sample_name_lims),
             shape=15, size=3, show.legend = FALSE)+
  stat_ellipse()+
  scale_color_manual(name=NULL,
                     values=c("blue", "red"),
                     breaks=c("CASE", "CONTROL"),
                     labels=c("case", "control")) +
  coord_fixed() +
  labs(x = "PC 1 (14.8%)",
       y = "PC 2 (8.5%)") +
  theme_classic()+
  theme(legend.position = c(0.95, 0.95))

For Adonis,I used this standard code:

#Adonis2 calculation of difference between species
#distance data from above: dist <- vegdist(f1, method = "bray")     

adonis2(dist~sample_name_lims, data = f, method = "bray")