Thirteen people were arrested during the Queen's visit to Wakefield for the annual Maundy ceremony.
The Queen's predecessors washed the feet of poor people
Police said two youths, aged 17, were being held on suspicion of threatening behaviour after apparently bursting balloons outside the cathedral.
Eleven other people were arrested for a range of offences including possession of offensive weapons, threatening behaviour and disorderly conduct.
West Yorkshire Police say the right action was taken for security reasons.
People in the crowd say that a number of balloons were burst as the Queen arrived to hand out Maundy coins to 158 pensioners.
A police spokeswoman said: "This disturbance was created as the Royal party arrived.
"It did confuse and frighten members of the public as the origin of the loud bangs was unclear.
"This could have been a firearm and in the interests of public safety our officers had to respond accordingly.
"There was no way of knowing until after the event what the cause was."
During the Maundy service in a ceremony to reflect the Queen's age on her next birthday, 79 men and 79 women received 79p in silver coins contained in a white leather purse.
The Ceremony of the Royal Maundy dates back to Edward I - previously the monarch would wash poor people's feet.
Maundy Thursday is remembered by Christians as being the time when Jesus washed the feet of his disciples.
The Queen made presentations to pensioners from various Christian denominations.
As well as the coins, the pensioners - the oldest of whom is 97 - were also presented with a second, red leather purse.
They contained a £5 coin commemorating the 200th anniversary of the Battle of Trafalgar and a 50p coin marking the 250th anniversary of Samuel Johnson's dictionary of English.
The 50-minute service was led by the Bishop of Wakefield, the Right Reverend Stephen Platten.
Afterwards, the Queen was joined by the Duke of Edinburgh for a 20-minute walkabout.
Thousands of people had gathered to greet her and cheered as the royal couple came out of the cathedral.
The pensioners who received the Maundy coins spoke afterwards of being included in the ancient ceremony.
Reginald Stone, 83, from Denby Dale, West Yorkshire, said: "I'm very pleased and so honoured to have been involved.
"The Queen didn't say much, but she did notice my Burma star. It was such a lovely occasion."
George Rickman, 70, from Wakefield said: "It was a great honour. She was absolutely lovely."