The mid-cap FTSE 250, considered a barometer of Brexit sentiment, fell 0.1% with furnishing retailer Dunelm dragging the most on a decline in its annual profit.
The domestically-focussed index was still reeling from losses after surging COVID-19 cases sparked new curbs on social activity in England, hitting shares of restaurant and pub firms.
Talks between Britain and the European Union on the relationship after the Brexit transition period concludes at the end of this year, which came to the forefront this week, hit a snag after Johnson's government refused to scrap a plan that could break their exit treaty.
The blue-chip FTSE 100 index shed 0.2% as gains in consumer discretionary stocks were offset by losses in healthcare and consumer staples.
"Markets are moving with heavy caution and we also see investors pulling back on some export-heavy names until they see concrete developments on the Brexit front," said Ronald Kaloyan, head of European equity strategy at SocGen.
A Reuters poll this week found chances of the two sides failing to reach a trade deal have jumped to 40%.
Supermarket group Morrisons fell 4.6% even as it said it expected profit growth for the full year, while table-top game maker Games Workshop Group topped the midcap index after it flagged a stronger quarterly profit.
British Airways-owner IAG closed flat as it launched a heavily discounted rights issue to raise 2.74 billion euros ($3.2 billion).
Homebuilders rose 1.2% after data showed house prices hit a four-year high in August, although the survey also sent a warning signal that the recovery could run out of steam.
(Reporting by Shashank Nayar in Bengaluru; Editing by Subhranshu Sahu, Uttaresh.V and Frances Kerry)
By Shashank Nayar and Ambar Warrick