R Error : some group is too small for 'qda'

tl;dr my guess is that your predictor variables got made into factors or character vectors by accident. This can easily happen if you have some minor glitch in your data set, such as a spurious character in one row.

Here's a way to make up a data set that looks like yours:

set.seed(101)
mytest <- data.frame(type=rep(c("monocot","dicot"),each=100),
                 mono_score=runif(100,0,100),
                 dicot_score=runif(100,0,100))

Some useful diagnostics:

str(mytest)
## 'data.frame':    200 obs. of  3 variables:
## $ type       : Factor w/ 2 levels "dicot","monocot": 2 2 22 2 2 2 ...
##  $ mono_score : num  37.22 4.38 70.97 65.77 24.99 ...
##  $ dicot_score: num  12.5 2.33 39.19 85.96 71.83 ...
summary(mytest)
##       type       mono_score      dicot_score     
##  dicot  :100   Min.   : 1.019   Min.   : 0.8594  
##  monocot:100   1st Qu.:24.741   1st Qu.:26.7358  
##                Median :57.578   Median :50.6275  
##                Mean   :52.502   Mean   :52.2376  
##                3rd Qu.:77.783   3rd Qu.:78.2199  
##                Max.   :99.341   Max.   :99.9288  
## 
with(mytest,table(type))
## type
##   dicot monocot 
##    100     100 

Importantly, the first two (str() and summary()) show us what type each variable is. Update: it turns out the third test is actually the important one in this case, since the problem was a spurious extra level: the droplevel() function should take care of this problem ...

This made-up example seems to work fine, so there must be something you're not showing us about your data set ...

library(MASS)
qda(type~mono_score+dicot_score,data=mytest)

Here's a guess. If your score variables were actually factors rather than numeric, then qda would automatically attempt to create dummy variables from them which would then make the model matrix much wider (101 columns in this example) and provoke the error you're seeing ...

bad <- transform(mytest,mono_score=factor(mono_score))
qda(type~mono_score+dicot_score,data=bad)
## Error in qda.default(x, grouping, ...) : 
##    some group is too small for 'qda'