Three times a week does sound like a bit much for shoulders. However, if the volume of each workout reflects the frequency your training shoulders(lower volume because of the frequency) you may be ok. Typically the most I’ve ever heard of someone training shoulders directly was twice a week. Remember that just because you’re not training shoulders doesn’t mean they aren’t being taxed.
Exactly on that last part you may not be targeting the shoulder but anything where your using your arms pressing pulling etc is working the shoulders s well.
if your able to hit it hard every other day id also check your intensity, may be lagging a bit