Prevent Snakemake from changing wildcards: sample for every rule
Placing two wildcards directly behind each other will make it impossible for snakemake to determine where one wildcard ends and the other begins. So it is simply taking the longest possible match for the first wildcard (sample) and then one character for the second (read). This will also cause the _ to be included in the wildcard value sample.

I'm assuming that this same pattern is used for the inputs of another rule to refer to the trim_galore_pe output. Hence why the _ is included in the wildcards there.

You might be able to fix this, simply by adding a _ in-between {sample} and {readgroup} in your first rule (and any other rules using this same pattern):

rule fastqc:
    input:
        os.path.join(config['Directories']['fastq_raw_dir'], '{sample}_{read}' + fastq_file_extension)
    output:
        html=os.path.join(config['Directories']['fastqc_dir'], '{sample}{read}_fastqc.html'),
        zip=os.path.join(config['Directories']['fastqc_dir'], '{sample}{read}_fastqc.zip')
    wrapper:
        "0.49.0/bio/fastqc"