I agree. I'm not 100% sure, as I had to add a few changes to your code to make it reproducible, @aleeie (there's no tidydata2 in the snippet you shared), but I think you're plotting over some of those points. Also note that you have a different jitter.width set for the violin and boxplots
library(tidyverse)
id <- rep(1:30, 3)
type <- rep(
c(rep("sca", 8), rep("fca", 22)), 3)
data <- c(
rep("Gene 1", 30),
rep("Gene 2", 30),
rep("Gene 3", 30))
set.seed(123)
value1 <- c(rnorm(8, 0.48, sd=0.41), rnorm(22, 2.5, sd=2.))
value2 <- c(rnorm(8, 0.14, sd=0.14), rnorm(22, 2.6, sd=1.8))
value3 <- c(rnorm(8, 0.3, sd=0.2), rnorm(22, 1.39, sd=1.2))
tidydata2 <- data_frame(data, id, type, value = c(value1, value2, value3))
pl <- ggplot(tidydata2, aes(x=data, y=value, color=type), alpha=1)
###################
# boxplot m/points + y_log10
###################
pl+ geom_boxplot()+
geom_point(position = position_jitterdodge(jitter.width = 0.13, jitter.height = 0, seed = 1234))+
ylab("Relative gene expression")+ xlab("")+
scale_y_log10()+
theme_minimal()+
annotate("rect", xmin=0.7, xmax=1, ymin=0.18, ymax=0.28, alpha=0.2)+
annotate("rect", xmin=2, xmax=2.3, ymin=0.085, ymax=0.12, alpha=0.2)
#> Warning in self$trans$transform(x): NaNs produced
#> Warning: Transformation introduced infinite values in continuous y-axis
#> Warning in self$trans$transform(x): NaNs produced
#> Warning: Transformation introduced infinite values in continuous y-axis
#> Warning: Removed 6 rows containing non-finite values (stat_boxplot).
#> Warning: Removed 6 rows containing missing values (geom_point).

###################
# Violin m/points + y_log10
###################
pl+ geom_violin(scale="width")+
geom_point(position = position_jitterdodge(jitter.width = 0.18, jitter.height = 0, seed = 1234), alpha=0.9)+
ylab("Relative gene expression")+ xlab("")+
scale_y_log10()+
theme_minimal()+
annotate("rect", xmin=0.7, xmax=1, ymin=0.18, ymax=0.28, alpha=0.2)+
annotate("rect", xmin=2, xmax=2.3, ymin=0.085, ymax=0.12, alpha=0.2)
#> Warning in self$trans$transform(x): NaNs produced
#> Warning: Transformation introduced infinite values in continuous y-axis
#> Warning in self$trans$transform(x): NaNs produced
#> Warning: Transformation introduced infinite values in continuous y-axis
#> Warning: Removed 6 rows containing non-finite values (stat_ydensity).
#> Warning: Removed 6 rows containing missing values (geom_point).

Created on 2018-09-17 by the reprex package (v0.2.1.9000)
If anything, it looks like the multiple points in the boxplot are off:
pl+
geom_point(position = position_jitterdodge(jitter.width = 0.13, jitter.height = 0, seed = 1234))+
ylab("Relative gene expression")+ xlab("")+
scale_y_log10()+
theme_minimal()+
annotate("rect", xmin=0.7, xmax=1, ymin=0.18, ymax=0.28, alpha=0.2)+
annotate("rect", xmin=2, xmax=2.3, ymin=0.085, ymax=0.12, alpha=0.2)
#> Warning in self$trans$transform(x): NaNs produced
#> Warning: Transformation introduced infinite values in continuous y-axis
#> Warning: Removed 6 rows containing missing values (geom_point).
