the charge min and max and missclevages are sometimes not working

### Description of the bug

@jpfeuffer @timosachsenberg @daichengxin I found one dataset that we search using msgf, here the command:

```
#!/bin/bash -euo pipefail
MSGFPlusAdapter \
-protocol automatic \
-in 01086_C01_P010738_S00_N03_R1.mzML \
-out 01086_C01_P010738_S00_N03_R1_msgf.idXML \
-executable $(find /usr/local/share/msgf_plus-*/MSGFPlus.jar -maxdepth 0) \
-threads 6 \
-java_memory 30720 \
-database "GRCh38r110_GCA97s_coding_proteins_19Jul23-decoy.fa" \
-instrument high_res \
-matches_per_spec 1 \
-min_precursor_charge 2 \
-max_precursor_charge 4 \
-min_peptide_length 6 \
-max_peptide_length 40 \
-max_missed_cleavages 2 \
-isotope_error_range 0,1 \
-enzyme "Trypsin/P" \
-tryptic fully \
-precursor_mass_tolerance 40.0 \
-precursor_error_units ppm \
-fixed_modifications 'Carbamidomethyl (C)' \
-variable_modifications 'Acetyl (Protein N-term)' 'Deamidated (N)' 'Deamidated (Q)' 'Oxidation (M)' \
-max_mods 3 \
-PeptideIndexing:IL_equivalent \
-PeptideIndexing:unmatched_action warn \
-debug 0 \
\
2>&1 | tee 01086_C01_P010738_S00_N03_R1_msgf.log

```

However in the file output I found the following id:

```

```
What could be the problem, this also happens for comet.

### Command used and terminal output

_No response_

### Relevant files

_No response_

### System information

_No response_