The Hyundai driver was reported to have started stage three late which left the Finn potentially facing a time penalty.
However, Lappi has since explained that he started the stage on time but was briefly delayed due to a miscommunication with the startline marshals.
Lappi headed to the stage start having lost hybrid power following a heavy landing in the day's opening test and was initially told he couldn't start the stage due to a flashing green light hybrid indicator on his i20 N.
"We were in time control already but it happened on the startline," Lappi told Autosport.
"I guess my green light flashed or something and they [the marshals] said I cannot start so I had to reverse from there and then we had some discussion with the marshal because the green light was on. I think they got scared or whatever because for a few seconds it was not on.
"There shouldn't be penalty because we were exactly on time."
Touted as one of the contenders for victory in Estonia, Lappi headed to mid-point service in fourth overall, 14.5s behind rally leader and Hyundai team-mate Thierry Neuville.
Lappi admitted it was frustrating to lose time to a lack of hybrid but took the blame for causing the failure. The unit is set to be reset ahead of Friday afternoon's stages.
"I was still without it [on the last stage of the morning] so we need a Compact Dynamics [WRC hybrid manufacturer] laptop," Lappi added.
"At the beginning [of stage two] the jump with the big drop, I had too heavy a landing it seems.
"Yeah, it is [frustrating[ but in the end I f***** it up myself. I was not expecting these things to happen but it was my mistake.
"It is frustrating but you just have to forget it and try to minimise the time loss. I really enjoyed the driving.
"The gaps are really small normally and it is tough to gain time back but anyway we did all we could. I was really flat out especially the last stage."
M-Sport's Ott Tanak clean swept the morning loop as the home hero recovered to 31st overall after being lumbered with a five-minute penalty after undergoing an engine change on Thursday.
