What is nCONFIG connected to? You certainly need this dedicated input pin high for normal operation. A pull-up should be fine. If this is floating then I'd expect the device to misbehave.
Pull-ups on CONF_DONE & nSTATUS are less critical. They won't prevent operation if they're missing but are needed if you wish to monitor their status externally.
Refer to the "MAX 10 Configuration Pins" on page 31 of the "
configuration user guide (
https://www.altera.com/content/dam/altera-www/global/en_us/pdfs/literature/hb/max-10/ug_m10_config.pdf)" and make sure all the configuration pins are connected appropriately. Have a good read of chapter 3 as well.
Sort nCONFIG and then check that all your power supply rails are good and within spec when cold.
Cheers,
Alex