I am assuming that other recording channels are working fine?
Yes, it could be the phone, but if the problem is not fixed when you change the phone then try the following:
If you have a spare recording port, can you move this phone to the spare and see what happens?
How are you recording the phone, from the handset (this does not always work very good and is the poorest recording quality)?
How long is the cable that goes from the logger to the phone (long cables with analog cause low/bad recording quality)?
If the recording works fine when you move it to another port, then the problem could be the ADIF card or ALI24 card, my guess would be the ALI24 but could be cabling depends on how you have the logger wired. If it has the same problem on the new port, then you should check the cabling.
Hope this helps.