I had exactly the same problem recently with rainwater collecting in the boot. Found over an inch of water sloshing around in the passenger side lower boot (under the removable plastic ‘bin’) and lots of condensation on underside of boot lid.
First checked boot lid seal, rear light seals and aerial - all seemed OK.
This suggested rain could be coming in through the small gap formed where my roof half-cover’s weighted tabs go across the boot lid seal. As Fluffy said above, don’t put the cover’s tabs IN the boot itself.
Have mopped up all the water I can, removed carpet and all trim in the boot and now drying them, using a tray filled with cat litter (aloe vera scented, no less!) to speed up moisture absorption.
Next heavy rain will tell whether the roof cover’s tabs were to blame, or whether water is coming from elsewhere…