Two records for one thing generally means one thing recorded twice, not counted twice.
The same record from two systems
Where a bank connection and an accounting system are both connected, a payment exists in both. They are matched by amount, date and description, and where any of those differ the match does not form.
The unified ledger sets out how the sources are reconciled into one set of figures, and what happens when a record cannot be matched.
The same customer entered differently
A customer created once in the field service system and once by hand, or spelled differently in each, is two records because nothing links them.
Merging them is done from customers and vendors, which keeps the history from both.
A payment and an invoice for the same work
Not a duplicate. An invoice records work billed and a payment records money received, and both belong in the record. They appear together where a view shows both.
Whether the total is affected
Usually not. Matching happens before figures are calculated, so a visible pair is frequently two views of one matched record rather than two counted amounts.
Where a total does look doubled, that is worth reporting with the amount and date — see a number looks wrong.
Genuinely paying twice
A different question, and one worth checking periodically — see duplicate payments.