When the Whisper transcribe of Youtube videos was introduced user preference for Youtube’s auto generated subtitles was not included.
There are multiple free ways to obtain Youtube subtitles and import them into LingQ yourself. If you’re after something more automated and using a PC these paid extensions for LingQ can be beneficial.
Rooster Youtube Playlist Importer
Rooster Youtube Video Overlay
In the overlay extension you can control when to split the video to bypass the import restrictions. Only supporting up to 150 mins right now though.