Transporter works however any given episode requires it to work. There was something about Ransom's bug and "Lover" that the Cerritos biofilter didn't catch on transport.
Um...I'd say yes as to how the Bio-Filter of the transporter works.
It's not about whether or not "bio filters" are calibrated or whether they're working properly. It's impossible for them NOT to work.
Here's how a transporter works.
Imagine the following.
In the kitchen of your home is a large lego castle made entirely of gray bricks. This is a person. The person has a parasite inside it in the form of an orange lego police car.
You are the transporter. Your job is to take apart the castle brick by lego brick, catalog every single brick you find and the position they were in, then rebuild the castle in the bedroom.
So you take apart the castle and you catalog your findings. As you take apart the castle piece by piece, you suddenly discover that there's an orange police car inside it.
You can take that apart and catalog it, too.
And you can certainly put it back together, brick by brick, once you move all the legos to the bedroom to reassemble the castle.
BUT YOU CAN'T POSSIBLY MISS IT.
Even if you didn't "notice" the orange car, when it came to cataloging the pieces, you'd have all these pieces that didn't fit. And you'd sure as hell notice them when you'd try to put the castle back together.
The transporter does the same thing for a person or any object. It literally deconstructs it at the subatomic level. It makes a record of every single atom and subatomic particle that it takes apart and exactly where they belong and then it reassembles those pieces in another location.
It can't just reassemble random unknown stuff just because it's there. It can't "miss" something that doesn't belong. Period. Otherwise, it would never, ever work. By definition, it has to "know" exactly what every single subatomic piece of the transportee is, what they are, what they do and where they go.
It could no more "miss" a parasite in someone's head than you could accidentally put that orange car back together without ever noticing it.