Cheap RFID tracking to log entry and exit?
In the first instance if you've never done a project like this, you need to learn the basics of RFID, in particular the different kinds of tags: if you have mismatched tags and readers it won't work.  Some tags support writing, some do not; there are various radio frequencies in common use.

Most people start with either


very cheap MF RC522 board (search for 13.56MHz SPI RFID MF RC522 on Ebay) and an Arduino, or
a USB-interfaced reader and a laptop
NFC tags and a suitable phone


In your case I would recommend the microcontroller version as it's the cheapest and you can put an oscilloscope wherever you want.  It's easy to play with and find out all the practical things you'll need to understand such as practical range and general "fussiness".
If you search on ebay for animal rfid you'll find many tags and readers.  The tags for insertion into animals are normally in glass tubes, the smallest of which is about 1.5 x 8 mm, which is I expect too big and heavy for the average bee.

The main difficulty is getting the tags small enough to go on a bee, which I understand is typically 13 mm long.

Things others have tried:


The first referenced paper uses 500&mu;m square tags which are powered by laser pulse.  (I didn't know about those either!)  p-Chips from PharmaSeq.
Another uses 4 mm round tags from Invengo.
Another paper used modified QR codes 2.1 mm square
Alibaba shows lots of results for nfc213 5mm, which looks very promising


So,


If your project is about bees, you'll have to solve that.  The first paper ("Automated montoring...") has a review of about a dozen other projects for tagging bees.
If your project is about automated tagging, perhaps you can select another animal.


Once you've got animals with tags, then you need to figure out the mechanical parts of getting the animals close to the reader.  If you can't mechanically force them to go past one by one, you'll need a reader which can read multiple cards at once.  (Some RFID technologies have a mechanism for the reader to silence responders in a structured way, in order to read multiple cards in a single place.)



Paper with laser-activated RFID:


"Automated monitoring reveals extreme interindividual variation and plasticity in honeybee foraging activity level" https://lab.igb.illinois.edu/robinson/sites/lab.igb.illinois.edu.robinson/files/inline-files/TenczarEtAl2014.pdf
Supplier: http://mail.pharmaseq.com/technology/


Paper with QR-type coding:


"Automated monitoring of behavior reveals bursty interaction patterns and rapid spreading dynamics in honeybee social networks"  https://www.pnas.org/content/115/7/1433
Supporting information https://www.pnas.org/content/pnas/suppl/2018/01/26/1713568115.DCSupplemental/pnas.201713568SI.pdf
Data http://www.beemonitoring.igb.illinois.edu/
Software https://github.com/gernat/btools


Paper with 4mm tags


"Honey bees increase their foraging performance and frequency of pollen trips through experience" https://www.nature.com/articles/s41598-019-42677-x
RFID Supplier https://channel.invengo.com/rfid-product-line/tags-inlays-comsumables/