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Struggling to get a reference from master's project supervisor

I have been applying for PhD positions since September 2019, and I think I must have applied for well over 40 by now, however I have only managed to get one interview offer. When I am able to get feedback on my applications or how I come across in informal meetings I am always told that I am a good candidate for a PhD and to keep on trying. In my application I am always sure to discuss what excites me about the project and the lab, how I think I can contribute to the field and to give specific details about why I would be a good fit for the specific university and/ or programme. I have also had my supporting statements reviewed several times by my university's PhD career advisor, so I really don't think it could be my supporting statement which is holding me back. I know my supervisor has failed to get at least some in on time, but institutions don't always give notification of receipt so I'm not sure how many times this has happened. I had a really good relationship with him other than this. I have tried to use another academic who was very lightly involved in my master's project however he is almost as bad at getting things in on time as my actual supervisor is, and the applications for which I used him all got ignored; I suspect because he wasn't my project supervisor. I really have no idea what to do about this but I am weary of talking to my project supervisor about it as I don't want to risk it coming across as me "blaming" him and then be unable to get a reference from him for different reasons.