It’s likely, because the symptom does match a previous case where the DS3231 RTC has to be replaced. It might also have to do with the PCB layout. Most DIY kits are made with DS1307. There was a small batch where DS3231 was adopted (to evaluate if it’s a better alternative). We built several example boards and they all worked well, so I assumed it’s all fine. A support email has been replied to you. Sorry again about the issue.
The warning and error you saw are all normal. These have to do with the behavior of the USBasp bootloader upon reset. You can ignore these messages.