The score was deadlocked at 2-2 after 20-time grand slam champion Federer gracefully claimed the opening set 6-3 before rain wreaked havoc and suspended proceedings on Saturday.
"The question marks surrounding his defeat today will only grow larger", Courier said in commentary on the Tennis Channel.
Federer, who had looked slightly off his game in his rain-disrupted third round match against Federico Delbonis, was his dominant self on Monday, winning 89 percent of his first service points while cracking six aces to just one double fault.
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Japan's Daniel won the first set on a tie-break before Djokovic, making his return from an elbow injury, took the second.
The 28-year-old had returned to play this winter after a five-month injury layoff due to a wrist injury. "I mean, I just completely lost rhythm, everything. Just struggled also a little bit with the health the last couple of weeks", said Djokovic, who appears to be dealing with the flu. "Very weird", he said of the loss to Daniel.
Djokovic scrambled to win the second set but looked rusty on stadium court, making 62 unforced errors compared to 29 for Daniel.
"You're still battling inside of your mind", he added, referencing his recent elbow surgery.
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"To me, it's not that surprising". Daniel went up 4-1 in the tiebreak before Djokovic got the minibreak back.
On the women's side, top-ranked Simona Halep came back to top 19-year-old Caroline Dolehide 1-6, 7-6 (3), 6-2 in just over two hours.
The ex-world No. 1 says he is yet to find his rhythm in practice as well but is glad he recovered sooner than expected from his surgery and that he managed to get on a match court this week.
In other men's matches, David Ferrer of Spain defeated Tennys Sandgren of the U.S. 6-2, 7-6 (7/3).
Novak Djokovic knocked out of Indian Wells
He is making a cautious return to the ATP Tour after stopping his 2017 season following Wimbledon, due to a right elbow injury. He extended his 2018 win streak to 13 matches and has only dropped three sets from 34 played this year.
Other seeded players who lost were ninth-seeded Lucas Pouille, who fell 6-4, 6-4 to Yuki Bhambri; 14th-seeded Diego Schwartzman, 7-5, 6-4 to Marcos Baghdatis; 21st-seeded Kyle Edmund, 6-4, 6-4 to Dudi Sela; and number 24 seed Giles Muller, 6-3, 7-5 to Pierre-Hugues Herbert.