Please have a look at this BIDS -> fmriprep transforms to (3.5 x 3.75 x 3.75) MNI space? - #2 by ChrisGorgolewski post and see if it explains what is going on.
Could you share the command line you used when running fmriprep? T1w needs to be listed in --output-space commmand line flag for outputs in T1w space files to be created.