I guess your are not using 6.2 series as this should raise and error message since issue10841

For me the problem is that the ORM create multiple record of the same target in Many2Many when there is code to prevent that. Indeed I think it is because target_ids should be made unique.
Also proteus should behave like the other client and keep only unique instance of record in Many2Many.

At the moment I published review395481002 related to invoices. Missing sales, etc...

Scenario:

1. Create taxes: Tax1 and Tax2
2. Create a product: Product1 Add Tax1 and Tax2 in account category
3. Create a account tax rule: "Rule1". Add a new line:
   3.1. origin_tax: None
   3.2. tax: Tax1
4. Create a party: Party1. Add customer_tax_rule related to "Rule1"
5. Create an invoice: party is Party1 and create a new product: product1

When do on_change_product, len(taxes) == 3 but client only show two taxes: tax1 and tax2

Now, open a trytond-console, and do same operation.

>>> transaction.set_user(1)
>>> User = pool.get('res.user')
>>> context = User.get_preferences(context_only=True)
>>> transaction.set_context(context)
>>> Invoice = pool.get('account.invoice')
>>> invoice = Invoice(1)
>>> InvoiceLine = pool.get('account.invoice.line')
>>> Product = pool.get('product.product')
>>> product = Product(1)
>>> invoice_line = InvoiceLine()
>>> invoice_line.invoice = invoice
>>> invoice_line.product = product
>>> invoice_line.on_change_product()
> /home/raimon/projectes/nandev/049296/trytond/trytond/modules/account_invoice/invoice.py(2197)on_change_product()
-> self.taxes = taxes
(Pdb) taxes
[1, 30, 30]
(Pdb) c
Pool().get('account.invoice.line')(**{'taxes': [1, 30, 30], 'unit': 1, 'party': None, 'unit_digits': 0, 'company': 1, 'product': 1, 'invoice_type': None, 'account': 1588, 'invoice': 1})
>>> from decimal import Decimal
>>> invoice_line.quantity = Decimal(1)
>>> invoice_line.unit_price = Decimal(1)
>>> invoice_line.save()
>>> invoice_line.taxes
(Pool().get('account.tax')(1), Pool().get('account.tax')(30), Pool().get('account.tax')(30))
>>> Invoice.update_taxes([invoice])
>>> invoice.taxes
(Pool().get('account.invoice.tax')(1), Pool().get('account.invoice.tax')(2))
>>> invoice.untaxed_amount
Decimal('1.00')
>>> [t.base for t in invoice.taxes]
[Decimal('1.00'), Decimal('2.00')]
>>> [(t.tax, t.base) for t in invoice.taxes]
[(Pool().get('account.tax')(1), Decimal('1.00')), (Pool().get('account.tax')(30), Decimal('2.00'))]

SQL:

# select id, line, tax from account_invoice_line_account_tax;
 id | line | tax 
----+------+-----
  7 |    3 |   1
  8 |    3 |  30
  9 |    3 |  30

Bug:
- Invoice line has three taxes: tax1, tax2 and tax2
- update_taxes(), the base from tax1 is 2.00 and not 1.00 (from total taxes in invoice line)

Reason:
New tax_ids are added in current list (extend). We need to set() unique taxes.

https://github.com/tryton/account_invoice/blob/6cb358db41d9c300934d8cfffa15bd04354509be/invoice.py#L2260