Ipswich took the lead after 39 minutes when Gary Roberts fired home a brilliant volley to stun the visitors.
Steve Howard headed in Morten Bisgaard's corner nine minutes after the interval to level for Derby.
Ipswich's Simon Walton was then sent off for two bookable offences before Lupoli snatched the points for Derby.
"We can't fault effort, we can't fault discipline but we can't forget we have a squad that needs to improve and players that need to improve.
"It may take years and years to achieve. We're six months in and you can't fix everything in six months."
Magilton had no qualms with Simon Walton's red card, but was bemused as to why Lee did not show Rams player Michael Johnson a second yellow.
"I'm going to see the referee. I've no complaints about our red card," he said.
"But explain to me why Johnson (who fouled Alan Lee with six minutes to go) stays on the pitch."
Derby: Bywater, Edworthy, Leacock, Michael Johnson, Boertien, Bisgaard, Jones, Barnes, Seth Johnson (Lupoli 60), Howard, Stead (Moore 90).
Subs Not Used: Bolder, Grant, Jackson.
Booked: Seth Johnson, Michael Johnson, Jones.
Goals: Howard 54, Lupoli 90.
Ipswich: Price, Bruce, Naylor, De Vos, Harding, Roberts (Sito 77), Garvan, Walton, Richards, Lee, Clarke (Williams 63).
Subs Not Used: Macken, Haynes, Supple.
Sent Off: Walton (59).
Booked: Walton, Garvan, Lee.
Goals: Roberts 39.
Att: 22,606
Ref: R Lee (Essex).