The large machines like RiteAid uses....called ScripPro
Those have a laser sensor and when the calibration key loosens with vibration,
those tend to OVERCOUNT Rxs. Hence the pharmacy loses money. The pills will fall thru the opening in twos or threes and be counted as one by the laser. (and I may add that people rarely call back to say they got over the stated amount. Perhaps only 10% in my experience notify the pharmacy of an overage)

Tabletop counters also may overcount, since they use light also.
However the Baker units may undercount. (they do not use lasers, and are pretty old fashioned and I haven't seen them recently in stores for this reason.
They make alot of drug dust and cause OSHA issues.

I have never seen a modern machine robot counter UNDERcount.

There are dishonet people in this world...however, pharmacists are less common.
The techs however, are often dishonest.
If and this is a big IF something dishonest is going on there, and stealing is bigtime, then they would be doing something to conceal it. Stealing from customers is dangerous and rather stupid to hide their own stealing. Because obviously customers notice and draw attention to the behavior. But it is possible.

You have to realize that the percentage of customers that lie to get what they want in pharmacies is very high. So over time pharmacists can get rather jaded. There is no excuse for "defensiveness" on the part of pharmacists however. Defensiveness suggests concealing of "something".

If you have that little vial that obviously cannot hold 60 tablets as appears on your label, I'd suggest you hold on to it, and call corporate headquarters and complain. Take a photo of it. On the bottle bottom is the size in drams printed on it. A 13 dr vial is obviously not going to hold 60 Allegra 180s.
Now, if it is only Allegra they are shorting you.... you need to call your insurance company and find out if Allegra benefits are limited. But if you are being shorted on other than Allegra, then you need to document and make a fuss. I sure would. We have a very liberal insurance and this limitation on Allegra caught me on vacation of all times. So I know it exists for others.
If you were limited this way, your label would read 30, not 60.

If something really bad is going on in that pharmacy, and corporate suspects it but cannot prove it yet, your complaint may be very crucial to getting it action there. So I really suggest you do that.

DO NOT complain further at the store local level. The manager may be part of any organized theft ring...and therefore
your complaint would be buried. (I have seen that happen! Trust me)