"using VNA with a probe" - that doesn't make much sense, can you provide more detail or a photo of your test setup?  

What was your test environment?  You can easily get unexpected results by having your antenna too near a metal surface, or more likely not having the same physical ground structure at your test fixture as you have in your application.  

Have you verified your test setup by measuring a known impedance?  

A crude technique I've used in the past is to use two identical antennas, one as source and one as receptor and then make a couple of S21 measurements with the setup and extract the parameters from there.  If you can get a decent S11 setup you'll probably get much better results though.  

John D

Hello,
In what range of frequency works your RF ID antenna?
Is the setup used by you calibrated somehow? Is there any offsets taken in consideration?
Maybe a picture  would be very helpful for us ,like zappedagain said in the above post.
Mishu