Bootsrapping, use case

Question

I have a very divers data set that I hoped to homogenize with bootstrapping to be able to compare the sample distributions. Here are two parameters each has the 95% confidence intervals for every experimental condition plotted with the original data in black and the bootstrap in red. I am wondering if the discrepancy of boostrapped vs original CIs disqualifies bootstrapping for this data?

Parameter 1:

Parameter 2:

Here are the counts for bootstrap (left) and original (right) for the sample data for each group.